Sam:
There is really never a case to change the stall interval.. It is a simple measure of application quality.
When something stalls, it simply means it took longer than 30 seconds - even if it does manage to return. While stall counts are especially useful when a transaction does not return, becasue the transaction trace cannot be completed in that case, the fact that the number is always increasing simply means the application has poor performance chartacteristics.
The 'job' for APM is to point out the performance issues and bottlenecks. Getting folks to fix them - that is another issue altogether.
Cheers,
Mike.