One floating point operation per second
One flops
Two giga- floating point operations per second
Two gigaflops
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?