Once you pass through some issues with submission it will work most of the time flawlessly for you, saving you lots of time.
This is basicly the main feature of the StockSubmitter and the reason it was made.
In your case I think the crash could mess things a bit, especially if you keyworded images before the crash. When the crash occurs, your changes made to metadata may be not saved.
Please first make sure images have their metadata filled correctly and then let the program run for a while with submission checkboxes turned on for the agencies you have uploaded images to.
Submission may be delayed after the upload because agencies usually need some time to process images uploaded by FTP.
Few agencies get images submitted right in the upload process (istockphoto, vectorstock, bigstockphoto in HTTP mode)
Colourbox does not need submit at all.
123rf needs only to start processing which StockSubmitter does if you have submission checkbox enabled for 123rf.
Most of the other agencies either upload-only for StockSubmitter or require delayed submission.
If you keep having problems with submitting images, don't hesitate to message me via Skype (landofrain). I can help you with any specific submit issue.