Same problem happened to me and I've found a solution..

Now HERE IS MY SOLUTION;
1) Change EnableClientScript settings to FALSE for each validation rule. (Custom or Regular doesn't matter)
This will post the page back and validate fields at server level.

2) Place your code which you would like to process, if all fields are valid to between followin if statement;
if Page.IsValid then
'Your code
end if

And this worked fine for me, I am positive it is going to work for you too,..

Thanks,
Mert..