We are using two Separate bug tracking tools (one for the core product and one for customisations). We want to merge them together because
1) we are finding that our customers need fixes before our core dept gets them merged into the core product
2) many bugs are fixed in the core product and our customers have not or choose not to upgrade. Often they don't know which build has the fix.
3) there is duplicate effort in both departments
Both teams are using Scrum