Thanks Luis for suggesting checking the machine and software with EtreCheck. I downloaded the application, ran it in standard mode with "No problem, just checking". The report is at the end of this message. One thing (which I could have easily spotted without EtreCheck) was that I had only 1 GB of free RAM (out of 16). So, to be sure, I then rebooted the Mac and opened preview.
Now, I can annotate the files normally!
But, I still have the issue that if I open another PDF file, it is appended to the previously opened one, even though "Open each file in its own window" is checked in Preview>Preferences>General.
Here is the EtreCheck report (before the reboot).
EtreCheck version: 2.9.11 (264)
Report generated 2016-04-18 11:22:25
Download EtreCheck from https://etrecheck.com
Runtime 1:30
Performance: Excellent
Click the [Support] links for help with non-Apple products.
Click the [Details] links for more information about that line.
Problem: No problem - just checking
Hardware Information: #
MacBook Pro (Retina, 15-inch, Mid 2015)
[Technical Specifications] - [User Guide] - [Warranty & Service]
MacBook Pro - model: MacBookPro11,5
1 2.5 GHz Intel Core i7 CPU: 4-core
16 GB RAM Not upgradeable
BANK 0/DIMM0
8 GB DDR3 1600 MHz ok
BANK 1/DIMM0
8 GB DDR3 1600 MHz ok
Bluetooth: Good - Handoff/Airdrop2 supported
Wireless: Unknown Battery: Health = Normal - Cycle count = 86
Video Information: #
AMD Radeon R9 M370X - VRAM: 2048 MB
Color LCD 1440 x 900
PLX2780H 1920 x 1080 @ 60 Hz
Intel Iris Pro
System Software: #
OS X El Capitan 10.11.4 (15E65) - Time since boot: about 9 days
Disk Information: #
APPLE SSD SM0512G disk0 : (500.28 GB) (Solid State - TRIM: Yes)
EFI (disk0s1) <not mounted> : 210 MB
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
Macintosh HD (disk1) / : 499.06 GB (244.78 GB free)
Core Storage: disk0s2 499.42 GB Online
USB Information: #
Apple Inc. Apple Internal Keyboard / Trackpad
Broadcom Corp. Bluetooth USB Host Controller
PIXART USB OPTICAL MOUSE
Thunderbolt Information: #
Apple Inc. thunderbolt_bus
Apple Inc. Thunderbolt to Gigabit Ethernet Adapter
Gatekeeper: #
Mac App Store and identified developers
Kernel Extensions: #
/Applications/Tunnelblick.app
[not loaded] net.tunnelblick.tap (20141104 (Tunnelblick build 4546) Unsigned - 2016-03-20) [Support]
[not loaded] net.tunnelblick.tun (20141104 (Tunnelblick build 4546) Unsigned - 2016-03-20) [Support]
/Applications/zoom.us.app
[not loaded] zoom.us.ZoomAudioDevice (1.1 - SDK 10.8 - 2016-03-04) [Support]
/Library/Extensions
[not loaded] com.Logitech.Control Center.HID Driver (3.9.1 - SDK 10.8 - 2016-04-05) [Support]
[not loaded] com.Logitech.Unifying.HID Driver (1.3.1 - SDK 10.8 - 2016-04-05) [Support]
[not loaded] com.m-audio.usb.midisupport.driver (1.4.1 - SDK 10.7 - 2016-04-05) [Support]
Startup Items: #
M-Audio Firmware Loader: Path: /Library/StartupItems/M-Audio Firmware Loader
Startup items are obsolete in OS X Yosemite
System Launch Agents: #
[not loaded] 7 Apple tasks
[loaded] 139 Apple tasks
[running] 92 Apple tasks
System Launch Daemons: #
[failed] com.apple.csrutil.report.plist
[not loaded] 41 Apple tasks
[loaded] 147 Apple tasks
[running] 99 Apple tasks
Launch Agents: #
[running] com.Logitech.Control Center.Daemon.plist (2015-09-19) [Support]
[loaded] com.google.keystone.agent.plist (2016-03-03) [Support]
[loaded] com.oracle.java.Java-Updater.plist (2016-01-13) [Support]
[not loaded] com.teamviewer.teamviewer.plist (2016-04-17) [Support]
[not loaded] com.teamviewer.teamviewer_desktop.plist (2016-04-17) [Support]
[running] org.macosforge.xquartz.startx.plist (2015-10-16) [Support]
Launch Daemons: #
[loaded] com.adobe.fpsaud.plist (2016-04-05) [Support]
[loaded] com.google.keystone.daemon.plist (2016-03-03) [Support]
[running] com.m-audio.usb.firmwareloader.plist (2014-07-24) [Support]
[loaded] com.oracle.java.Helper-Tool.plist (2016-01-13) [Support]
[loaded] com.teamviewer.Helper.plist (2016-02-01) [Support]
[not loaded] com.teamviewer.teamviewer_service.plist (2016-04-17) [Support]
[loaded] net.tunnelblick.tunnelblick.tunnelblickd.plist (2015-10-28) [Support]
[loaded] org.macosforge.xquartz.privileged_startx.plist (2015-10-16) [Support]
User Launch Agents: #
[loaded] net.tunnelblick.tunnelblick.LaunchAtLogin.plist (2015-07-10) [Support]
User Login Items: #
Flux Application (~/Applications/Flux.app)
iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
Dropbox Application (/Applications/Dropbox.app)
SpeechSynthesisServer Application (/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks /SpeechSynthesis.framework/Versions/A/SpeechSynthesisServer.app)
XQuartz Application (/Applications/Utilities/XQuartz.app)
Emacs Application (/Applications/Emacs.app)
Activity Monitor Application (/Applications/Utilities/Activity Monitor.app)
Other Apps: #
[running] com.etresoft.EtreCheck.131552
[running] com.tableausoftware.tableaureader.130592
[running] com.wolfram.Mathematica.56992
[running] net.tunnelblick.tunnelblick.62432
[loaded] org.gnu.Emacs.5472
[running] org.herf.Flux.72992
[running] org.macosforge.xquartz.X11.8352
[loaded] 387 Apple tasks
[running] 243 Apple tasks
Internet Plug-ins: #
FlashPlayer-10.6: 21.0.0.213 - SDK 10.6 (2016-04-08) [Support]
QuickTime Plugin: 7.7.3 (2016-03-12)
Flash Player: 21.0.0.213 - SDK 10.6 (2016-04-08) [Support]
Default Browser: 601 - SDK 10.11 (2016-03-12)
o1dbrowserplugin: 5.41.3.0 - SDK 10.8 (2015-12-16) [Support]
googletalkbrowserplugin: 5.41.3.0 - SDK 10.8 (2015-12-11) [Support]
Mathematica: 10.0.0 - SDK 10.10 (2016-03-03) [Support]
JavaAppletPlugin: Java 8 Update 74 build 02 (2016-02-17) Check version
User internet Plug-ins: #
ZoomUsPlugIn: 3.5.40307.0206 - SDK 10.11 (2016-03-04) [Support]
Safari Extensions: #
AdBlock - BetaFish, Inc. - https://getadblock.com (2016-03-31)
DuckDuckGo - DuckDuckGo - http://duckduckgo.com (2015-10-30)
Reload Button - John Siracusa - http://siracusafamily.org/safari/extensions/ (2015-10-30)
Translate - SideTree.com - Apps for Mac and Web - http://SideTree.com/extensions.html#Translate (2016-01-31)
URL Rewrite - Sijmen Mulder - http://github.com/sjmulder/urlrewrite-safari (2014-08-07)
3rd Party Preference Panes: #
Flash Player (2016-04-05) [Support]
Java (2016-02-17) [Support]
Logitech Control Center (2015-10-30) [Support]
TeXDistPrefPane (2015-10-22) [Support]
Time Machine: #
Auto backup: YES
Volumes being backed up:
Macintosh HD: Disk size: 499.06 GB Disk used: 254.28 GB
Destinations:
My Book 2TB [Local]
Total size: 2.00 TB
Total number of backups: 2
Oldest backup: 02/04/2016, 13:51
Last backup: 02/04/2016, 15:39
Size of backup disk: Excellent
Backup size 2.00 TB > (Disk size 499.06 GB X 3)
Top Processes by CPU: #
21% WindowServer
2% fontd
1% Finder
1% kernel_task
0% WolframKernel(2)
Top Processes by Memory: #
2.05 GB Preview
1.72 GB kernel_task
1.17 GB com.apple.WebKit.WebContent(11)
508 MB Finder
426 MB Mail
Virtual Memory Information: #
1013 MB Free RAM
15.00 GB Used RAM (2.80 GB Cached)
3.61 GB Swap Used
Diagnostics Information: #
Apr 17, 2016, 03:53:25 PM ~/Library/Logs/DiagnosticReports/fontd_2016-04-17-155325_[redacted].crash
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ ATS.framework/Versions/A/Support/fontd