This doesn't happen in my speech, I certainly pronounce both <a>'s as [a] in "niania". [ɛ] is different, it certainly becomes [e] after palatalized consonants. I agree that people cannot tell the difference intuitively, though.
It happens more in fast speech. If you draw out the vowel - as people tend to when they are trying to get a better feel of it - it will end up at [a] even if it doesn't start there. I suspect you'd need to actually record it and then look at the formants to tell for sure.
