This seems to be a problem on most boards regardless of brand mATX or ATX. All boards should have at least 3 fan headers that are fully functional, RPM, speed control, full bios support. Higher end boards should have 6 or more. What really sucks is that review sites never investigate fan header specs or function in their reviews. On top of that if you research before selecting a board its near impossible to prove what a given boards fan header capabilities are.
Downloading the manual for all potential boards and then spending hours reading does not guarantee success. My latest build using a GA-X58A-UD3R rev 2 has an ass load of fan headers. Well guess what only the 4 pin CPU and one 3 pin header are fully functional and bios support is piss poor. If fan headers are not fully functional they should not be on the board! Board manufactures need to pull their heads out of their arses.
Bill