When the collission light blinks on a network hub, that doesn't necessarily indicate a problem. It is possible that you simply encountered a bug in the software that was unrelated to the amount of network traffic. Then again, it might have been precisely that, I don't know: there was another bug report of synch errors when synching on a busy network.

When using beta versions of emplode, always do your work/synchs in small batches.

Also, it would be a good test to downgrade to 1.03 and do the big synch, just to rule out other problems.