There is no problem with PBP Interrupts in any program be it small or large.

You will have remembered (if you read the PBP documentation) that in PICBasic a jump to interrupt (ON INTERRUPT command) is only executed AFTER the current PICBASIC command has completed. So, for example, if an interrupt occurs at the start of say a PAUSE 5000 command, the jump to interrupt will not occur for almost FIVE SECONDS!! Some PBP instructions take a long time to complete, and those should be avoided if you are waiting for an interrupt which needs to be serviced quickly.