One has always seen this from time to time on any system, and I do see it once in a while on Linux. I believe this happens when a second SIGINT is received while quit-flag is still set. That may just mean that the whole path of the first signal getting handled, the quit getting up to Lisp and being handled, is a bit slower so that it's done all done by the time you do a second C-c and a second SIGINT interrupts that path. Or it could mean something else like the original signal is delayed in reaching Emacs for some reason so that it appears to have taken a long time to process.
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