This is going to sound crazy, but I also experienced random-seeming problems where a capture is often instant, but can often be delayed by a few seconds as well. It's seemingly not related to processor or IO spikes either. Now here is the crazy part. I think it's caused by systray icons (not even necesarrily ScreenshotCaptor, but another application) being involved in some sort of blocking operation.
What I noticed is that my screenshots are usually instant. But, I have a systray mail checking program that checks every few minutes. When it does this the icon changes to a lightning bolt, it does some involved operation where it logs into a server and checks for mail, and then the lightning bolt disappears. Whenever the lightning bolt is active, ScreenshotCaptor's icon will go red to start a capture, but the capture will not occur until the lightning bolt disappears.
Since my mail app (PopTray) does several accounts in a row, every 5 minutes it will cycle as like so:
Normal state (~5 minutes) -> Bolt (5 seconds) -> Normal (1 second) -> Bolt (5s) -> Normal (1s) -> Bolt (5s) -> Normal (~5 minutes)
If I capture (or spam capture) during bolt 1, the systray icon will stay red until the bolt vanishes, capturing nothing, then rapidly capture many images in that 1 second gap, then continue to "block" screenshots until the next gap, etc. As long as there's no bolt there everything is fine.
I realise this sounds crazy... how in the hell is a POP mail checker stopping screenshots? But I believe the systray is the key. That is the only space these two applications share, and something in there is causing one to block the other.
This may not be the reason for your problem, but it's something I noticed and it's a possibility.