Sorry for so many edits,
I first posted and said I had a database error related to utime, causing the server to go into restart loops.
I then snipped the post, because I was able to look at the database and found that it was used by many other services within gmod, and couldn't be sure utime was at fault.
I have since looked at it and after changing something that I thought to be an error, my server is now working again, it was in fact related to utime.
On the utime table I have 1000 entries.
There is another table called "sqlite_sequence" and it lists utime among other things like sui_ratings, then there is a "seq" column, this column seems to contain the number of entries for each table it lists. utime's entry was 1644.
Changing this to match the actual table 1000, seemed to fix things.
I still don't know if utime is to blame or if something else is. Or if this is a permanent fix. I thought I'd report it none the less.