I believe if you "force alphabetical" upon image sequence import, you will be fine regardless of how many images happen to be in your sequence folder at one time or another. Also you can turn off auto-reloading in prefs.
has that been changed since AE CC?
I never had any issues importing a sequence. Also, I noticed that I really need to pick the first frame of a sequence. In this case, blablag.750.jpg. That was never been an issue. In the previous versions, you could always pick a random frame and AE just automatic fixes the start and end frame of the sequence. Now you have to be really carefull. Also, this doesn't explain, why AE just shows up the sequence perfectly fine, but on a restart of AE of a background render, things goes wrong.
I know auto-reload is much better in CC. Lots of QT errors before we figured out a workaround, but haven't experienced the trouble you are describing. Did changing your prefs or ticking "force alphabetical" help?
Today, we released the After Effects CC (12.1) update, which fixes this bug with the Timecode effect and some bugs with regard to image sequences.
Let us know how it works for you when you've tried with the updated version.
Thnx! Great, yes the timecode fix is working! I can leave AE CS6 now and move back to CC. ;-)
As for the time sequence, I didn't try that yet, but I have a project the next few days which I will heavily make use of importing image sequences.