Fairly recently, someone near me was talking about "megaflops per second". I made a joke about computing while falling into informational singularities. It did give me a fun mental diversion, trying to imagine a physics where computational speed was tied to some sort of data density, and then I realized that Vernor Vinge sort of got there first, with _Fire Upon the Deep_.
One flops
Two giga- floating point operations per second
Two gigaflops
When the pluralization happens in the middle of the acronym it becomes weird -- one FLOPS, two FLOPsS?
Anyway, you're right, they would all get an S at the end either way.
A better example would be "captcha." You'd say "two captchas," not "two captcha" or "two captscha."
For a less polite example that works the same way, consider MILF.
Two gigaflosps?