Try switching the redstone modes anyway, if you haven't already, at least on the buses and emitters on the machines that are giving you problems.Thanks for your answer.
This is my setup
http://prntscr.com/4fepsf
I activate the procss of running the machine by level emitters on the export busses.
I dont use redstone on the machine themselfe.
So it does not matter if i switch the settings in the bus and the emitter.
http://prntscr.com/4feqan
http://prntscr.com/4feqe3
Here's my reasoning:
Say you've got an export bus set to run without a redstone signal, and a level emitter set to emit a signal when there are more than however many items in the network.
There are more than however many of those items in the network, so the emitter is on and the bus was off.
Now, as the network boots up after having something added to it, I'm guessing that the AE activates all the machines in it in some arbitrary order. The export bus might come online before the level emitter, so it's not being given a signal quite yet. Since it's not being turned off (yet), it might decide to go ahead and export a stack of items. Then, later, AE gets around to activating the level emitter, which then starts emitting a redstone signal and prevents the bus from exporting any more items. But, it had already exported that stack or items, and there's nothing it can do about that now.
However, if you swap the redstone modes, the bus won't turn on until it actually gets a redstone signal from the level emitter. The worst that could happen in this case, since the bus defaults to "off" instead of "on", is the bus might take a bit longer to actually start running if you reboot the network while it's trying to produce more items.
If this fix works, I would call this a minor bug that I would recommend reporting to Algorithm if AE1 was still being actively updated. But, since he's moved onto AE2 now, I probably wouldn't bother. Unless, of course, the bug still exists in the latest AE2 release... [Requires testing with export buses, level emitters, and chests.]