@damienbarrett did you turn on Patch Reporting in 9.96? I've read some other threads about people having issues after having enabled patch reporting in 9.93 and 9.96. Maybe your database size issue is related to that. Just speculating here though.
@damienbarrett typically that database table is used when you upload a package when using a JDS. When you upload trough Casper Admin and are using a JDS it uploads it to the JSS Tomcat app which then stores it in that table in the MySQL database then pushes it down to the JDS. It should then clear out that table. This is a goofy architecture. When we were trying using the JDS early in we ran into this same issue constantly and had to manually flush that table from MySQL because the JSS would neglect to clear it out.
We got tired of it and switched to another deployment option.
Yes, this is related to JDS synching. I enabled another JDS at the same time I upgraded to 9.96 and that's causing the problem. I found the directions for truncating the offending SQL table and will do so tomorrow when back at work. This is indeed a clumsy architecture for synchronizing...not sure what JAMF is thinking here.