That's strange, i never thought getting to full mana/hp would waste queued regen from current flasks, thought it'd just continue acting as buffer against incoming damage/mana expenditure even in that case.
In that case In it's current implementation script can't reliably check if flasks expire from getting respective resource to full, sure i've added a simple check
Code:
if (currLifeRatio=1)
WindowQueuedFlaskEffects[k].hpQueueEndtime:=A_TickCount
if (currManaRatio=1)
WindowQueuedFlaskEffects[k].ManaQueueEndtime:=A_TickCount
But script only checks your hp/mana every so often and it's likely to not catch you at exactly 100% cause you may get hit a bit or cast something right before script reads memory values = detection screwed up.
And if you add some room for error e.g. treat 97-98% resource as full and reset timers you're likely to instead incorrectly reset timers when you shouldn't, waste flasks, not get your regen anyway and die.
Flasks like granite give you a buff and that could probably be memory-read but hp/mana ones don't, at least visually.
All in all this issue is not likely to get addressed any further by me.