Some accented characters showing on uppercase are missing in their lowercase counterpart and vice-versa

Question

I constantly swap between English - US (for programming) and Portuguese - US International (for writing), mostly because a few symbols expect a letter in the US International layout (e.g. ' " ` ^ ~) and it's cumbersome to type space afterwards or something else. Right after booting, my keyboard behaves normally on Windows 7.

Programs save the current layout and this usually works alright, since I don't care for US Intl. on my code editor, but everywhere else I switch a bunch of times.

And there lies the problem: after a few hours, some symbols stop showing on lowercase characters while still working on uppercase ones and vice-versa. However, on Windows' virtual keyboard I've seen no problem whatsoever.

I hope what comes next doesn't seem like I'm joking, because I am really typing/clicking all those combinations and it makes absolutely no sense. Nonetheless, for example:

á é í ó ú a o e o keyboard
A E I O U Ã Õ Ê Ô also keyboard
á é í ó ú ã õ ê ô virtual keyboard, where it gets weirder
Á É Í Ó Ú Ã Õ Ê Ô virtual keyboard, again

This is sort of frustrating because I can't find an answer anywhere, even trying to query for every possible phrasing for this particular problem. I can't see a pattern, and apparently my keyboard switches are working fine (as it shows on my previous examples). But in combination with a specific capitalization, it just doesn't work.

These are the two windows for input settings that I found relevant, there's nothing there that I haven't tried (even the key sequences suggestion I found here on SU):

Enabled languages and their respective layout
Key sequences for layout swapping

Thanks in advance!