Well I'm not 100% sure but I think we've found the problem. The system we use is interconnected with several other systems some of which are a bit old. It looks like the Windows Heap was somehow causing issues, technically the software that uses it. We solved it by running a Microsoft Heap analyzer product which saw it getting full. I don't understand how that could effect SQL but somehow it looks like it was. The Heap problem is on another machine but communicates to SQL.