DT,
You did say you were woking in Cycle mode when this happens.. correct?
Could "note off" messages be missed?
In Logic's SETTINGS, go to MIDI and "Chase" There should be some settings at the bottom related to Cycle Jump. I would have "Notes" selected as well.
Also, in Logic's Preferences under the General Tab select Cycle and look at the settings there.
In case it's preferences related definitely give this a try:
Delete the Logic 10 preferences file AND the shared control surfaces file.
(Note: be sure and use the tilde ~ in the path name.)
In the Finder, choose Go > Go to Folder from the menu.
Type ~/Library/Preferences in the "Go to the folder" field.
Press the Go button.
Remove the com.apple.logic10.plist file from the Preferences folder. Note that if you have programmed any custom key commands, this will reset them to the defaults. You may wish to export your custom key command as a preset before performing this step. See the Logic Pro User Manual for details on how to do this.
If you are having trouble with a control surface in Logic Pro.
then delete the com.apple.logic.pro.cs file from the preferences folder.
Be sure and remove both files. (with Logic not running of course) next time Logic boots these files will be recreated.