"I'm having the same problem as some other people here. After updating to 2.6.5 it seems that Arq is uploading my whole folder instead of just the files updated/uploaded between March 7 and now..."
Whatever it is that happened in the last couple of versions of Arq, the results can be, well, terrible. I was mostly away from my computer after upgrading to 2.6.5, and didn't catch what was happening as it went merrily on its way: *every* backup I had for the last 18 months was wiped out, as Arq (I can only guess here) reuploaded fresh copies of nearly everything. Arq then trimmed the data to within my storage budget (100 GB).
I now have no backups prior to March 7. Nothing. 18 months of incremental backups wiped clean, leaving only incremental backups for March 7, 28, 29, 30, and 31. My guess is that the same thing has happened on my spouse's machine, but I'm not home to be able to check that or stop the slaughter. I expect our Amazon S3 bill this month to inflate accordingly.
That's, er, pretty irritating. Not catastrophic: Arq is one of my backup-of-backup methods. I have Time Machine backups for all of this data which are probably sound for this period. And it's unlikely that I'll need access to a version of a file changed umpteen times since last October. But I'll confess that I'm a little less confident of the Arq/S3 model than I was before this AM.