This is really getting annoying. For now I'm back to AviSynth 2.5 because it happens less than with v2.6, and copy back v2.6 whenever I need to do other work with AviSynth. Switching back and forth like this isn't ideal.
Also, the performance improvements are kind of meaningless when it only applies for "some" content and it occasionally lags like this. The performance settings have to be adjusted to the lowest common denominator, which means that even if a single video doesn't benefit from the 40% improvements, none of the others of similar resolution can enjoy increased settings either.
Perhaps this issue is showing up more for me because I tweaked my settings to keep the CPU between 80-100%. If it was running at 50% (as default), then I wouldn't notice these lags as much.