All,
I have a set of install scripts. They’re nested in a tree-like structure.
When I execute a script using F5, I get a pop-up “Processing Script” with a time indicator.
While the script executes the pop-up is refreshed several times:
it disappears, then reappeaars, with the elapsed time counter reset to 0.
This is for Toad 12.8.0.27.
By the time the procedure ends several minutes have passed, but the pop-up indicates 5 seconds 
What additional info do you need to fix this issue?
Remark: The issue occurs intermittently, though mainly when a new process is being started on my Windows laptop.
E.g. the mouse monitor emits its pop-up I should take a short break, or I start another Toad instance.
I hope this helps.
Addition: I’m not so sure about my previous remark. It also looks like this happens when the script being executed generates a warning message.
It’s hard to tell coincidence from causality 
One more remark: I was running Toad in debug mode (ScriptDebug=1), but I’d forgotten I turned it on about a week ago.
Could it be that the debug mode being active was causing the issue?
One more remark: now that I have turned off debug mode, the script executes much faster (no surprise). The resets, too, fly by at a much higher pace. I no lnger can see the pop-up disappear and re-appear, but I can see the execution time counter reset. This seems to happen at the same point in the script every time I execute it. (I need to run this on 14 databases).
This all hints at an internal cause, rather than external events. Primary candidate (to the unaided eye) would be the message “Warning: compiled but with compilation errors”.