With OCS, you can set it up so that the submission process has two rounds: abstract and then paper submission. This is available from the Conference Manager's User Home --> Conference Setup --> Step 2. Submissions. Under Submission Materials, you can choose Abstract followed by Presentation; the original submission process will only require an abstract, and the user will be prompted at the end of abstract review to submit their full paper. Of course, if you're already mostly through the submission process, I wouldn't worry about changing; the steps you are currently using should also work.
In regards to the files not uploading: you mentioned you had checked your max filesize; what is it? Are the problem files big in relation to the others? Have you also checked PHP's memory_limit (a quick search on the forum will provide some relevant discussion)? Sometimes that can interfere with uploading larger files.
I would also suggest looking at OJS' FAQ, as some of the points might be relevant here, specifically permissions, and the advice on error-checking. Please get back to us if you do find errors. The FAQ: viewtopic.php?f=8&t=2481
I haven't personally heard of any problems with spam filters, but I all ask the team. I'm guessing that there's probably nothing you can do on your end though.
And can you provide any more detail on your user login problem? If you can't replicate it yourself, it may be a user-specific issue.