So even with sophos removed, I still get sites with the green dot going off and on seemingly randomly. But even with the dot off, the site is still accessible over the internet:

Here is the latest test without sophos:
EtreCheck version: 2.6.6 (226)
Report generated 1/4/16, 4:44 PM
Runtime 1:34
Download EtreCheck from http://etrecheck.com
Click the [Click for support] links for help with non-Apple products.
Click the [Click for details] links for more information about that line.
Hardware Information: (What does this mean?)
Mac mini (Late 2014)
[Click for Technical Specifications]
[Click for User Guide]
Mac mini - model: Macmini7,1
1 2.6 GHz Intel Core i5 CPU: 2-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: en1: 802.11 a/b/g/n/ac
Video Information: (What does this mean?)
Intel Iris
Display 1280 x 1024 @ 60 Hz
System Software: (What does this mean?)
OS X Yosemite 10.10.5 (14F1509) - Time since boot: about one hour
Disk Information: (What does this mean?)
APPLE SSD SM0256F disk0 : (251 GB) (Solid State - TRIM: Yes)
EFI (disk0s1) <not mounted> : 210 MB
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
[redacted] (disk1) / : 249.78 GB (198.06 GB free)
Core Storage: disk0s2 250.14 GB Online
USB Information: (What does this mean?)
Seagate BUP Slim Mac SL 1 TB
EFI (disk2s1) <not mounted> : 210 MB
S3_Backup (disk2s2) /Volumes/S3_Backup : 999.86 GB (692.32 GB free)
ASIX Elec. AX88179
Apple, Inc. IR Receiver
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
Thunderbolt Information: (What does this mean?)
Apple Inc. thunderbolt_bus
Gatekeeper: (What does this mean?)
Mac App Store and identified developers
Kernel Extensions: (What does this mean?)
/Library/Extensions
[loaded] com.asix.driver.ax88179-178a (1.2.0 - SDK 10.9) [Click for support]
[not loaded] com.asix.driver.ax88772 (1.3.0 - SDK 10.9) [Click for support]
Startup Items: (What does this mean?)
MySQLCOM: Path: /Library/StartupItems/MySQLCOM
Startup items are obsolete in OS X Yosemite
Launch Daemons: (What does this mean?)
[loaded] com.adobe.fpsaud.plist [Click for support]
[loaded] com.bombich.ccchelper.plist [Click for support]
[running] com.mysql.mysql.plist [Click for support]
[loaded] homebrew.mxcl.php56.plist [Click for support]
User Launch Agents: (What does this mean?)
[loaded] com.google.keystone.agent.plist [Click for support]
User Login Items: (What does this mean?)
iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
X-Assist Application Hidden (/Applications/X-Assist/X-Assist.app)
Other Apps: (What does this mean?)
[running] com.apple.DeviceManagement.postgres - No signature!
[loaded] com.apple.collabd.expire - No signature!
[loaded] com.apple.disks.smart.status - No signature!
[loaded] com.apple.salearn - No signature!
[loaded] com.apple.saupdate - No signature!
[running] com.apple.server.httpd - No signature!
[loaded] com.apple.server.v2.stats - No signature!
[running] com.apple.xpc.launchd.oneshot.0x10000000.Server - Invalid signature!
[running] com.etresoft.EtreCheck.121584
[running] com.ortabe.xassist.41496
[running] org.amavis.amavisd
[loaded] org.amavis.amavisd_cleanup
[loaded] org.calendarserver.agent
[loaded] org.calendarserver.archive
[running] org.calendarserver.calendarserver
[loaded] org.calendarserver.relocate
[running] org.clamav.clamd
[running] org.clamav.freshclam
[running] org.dovecot.dovecotd
[loaded] org.dovecot.fts.update
[running] org.isc.named
[running] org.postfix.master.active
Internet Plug-ins: (What does this mean?)
FlashPlayer-10.6: Version: 20.0.0.267 - SDK 10.6 [Click for support]
QuickTime Plugin: Version: 7.7.3
Flash Player: Version: 20.0.0.267 - SDK 10.6 [Click for support]
Default Browser: Version: 600 - SDK 10.10
3rd Party Preference Panes: (What does this mean?)
Flash Player [Click for support]
MySQL [Click for support]
Time Machine: (What does this mean?)
Skip System Files: NO
Auto backup: YES
Volumes being backed up:
Server3: Disk size: 249.78 GB Disk used: 51.72 GB
Destinations:
Seagate Backup Plus Drive [Local]
Total size: 999.86 GB
Total number of backups: 83
Oldest backup: 5/8/15, 4:17 PM
Last backup: 1/4/16, 4:03 PM
Size of backup disk: Excellent
Backup size 999.86 GB > (Disk size 249.78 GB X 3)
Top Processes by CPU: (What does this mean?)
121% mdworker(2)
5% WindowServer
3% fontd
1% kernel_task
1% ScreensharingAgent
Top Processes by Memory: (What does this mean?)
1012 MB kernel_task
492 MB mysqld
328 MB clamd
180 MB mds_stores
115 MB amavisd (master)
Virtual Memory Information: (What does this mean?)
7.35 GB Free RAM
8.65 GB Used RAM (4.88 GB Cached)
0 B Swap Used
Diagnostics Information: (What does this mean?)
Jan 4, 2016, 03:21:23 PM Self test - passed
-----
That was run a while ago, but the time at the bottom is not the time of the test. I ran it again and the time is the same in that test. But this was different:
Top Processes by CPU: (What does this mean?)
5% WindowServer
3% fontd
1% ScreensharingAgent
1% kernel_task
1% screensharingd
Thankls!