In many cases you actually need to run dual HDMI connections to get full resolution.
What video cards are you using?
What windows drivers are you using?
What linux drivers did you use?
What DP to HDMI adapter are you using?
What EDID information does Windows see?
Were you running Linux on exactly the same computer with the same hardware and cabling?
Exactly what are the symptoms?
Are lower resolutions available?
Marantz SR7009/7.1.4/FH+TM/DefTech PM1000/LCR+TM amped