I don't know why this would be happening to you regularly, as it only happens to me when the site goes down temporarily. However, there is a great way to make sure you do not lose your comic...
If it fails to submit, you should end up with a huge URL showing on your browser, including all the dialogue and narrative and everything else in your strip. Select it all, copy it (Ctrl+C), and paste it (Ctrl+V) into Notepad or something similar. When SC.com appears to be back up again, paste the back into your browser and whack enter.
This has worked for me every time I have tried it.
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