Do you have sufficient free space both disk space in the repository and the free space on the DB instance. If either of these are running low then this can slow the projects that are running low on resources and eventually cause loss of data. It is recommended that the DB be set to unlimited growth to alleviate this issue. I would assume that it was one of these resources from your statement that it is only certain projects. If it were all projects then the Heap size could be getting overrun.