The higher that tower of turtles, the stronger the confidence.
The proof checker can be ran several times to account for faults. Then you don't need to run it at all (it's proven). And you can use another proof checker (or that proof checker itself) to prove that the proof checker works. Etc.
Now there's the problem of the compiler, which gives a upper bound on the confidence you can have: if there's a bug in it, you're screwed even with a correct algorithm.
> Even if full mathematical code analysis shows it to be so
Come to think of it, that may not be possible for lots and lots of algorithms —whose mathematical security is only conjectured to begin with. Thanks for pointing that out.