I wonder if that 1 second blip is actually something else. Like, if you have any Razer hardware, that comes with a lot of rubbish software these days... like that game scanner that needs 1/4 of a processor the whole time for some reason.
Maybe it's worth trying a gradual change to the timer, like:
nt#=GetFrameTime()
if Elapsed#<nt# then Elapsed#=Elapsed#+0.001
if Elapsed#>nt# then Elapsed#=Elapsed#-0.001
Just guessing here - but if you change the 0.001 part to a suitable value, and use Elapsed#, maybe it'll help to hide the sharp changes in frame time - so if there is a delay somewhere it won't necessarily get a chance to affect things, because the actual Elapsed# value is gradually changed to suit GetFrameTime()
With some refinement and some time to ramp up (or a workaround to allow sharp changes at the start) it might make a difference.
One other thing to look at is your sound files - maybe there's a big awkward sound file that has to be buffered or something before being played. I'd work backwards, disabling things until the delay jump disappears - I have seen similar things with my last AppGameKit project, these days I just try to stick with fixed frame rates.
I am the one who knocks...
