Had the same issues (beeps) when trying to install 2x2G Samsung memory modules in replacement of 2x1Gb Samsung that were in my Mini from the factory. Attempts to reset PRAM/NVRAM were not successfull. But, maybe, my failure here is due to the fact, that I have PC keyboard (Sorry Apple, I have to use two desktops simultaneoulsy - with KVM - and PC came here first :-)).
In my case Mini booted ok with the following configs: 2 old 1GB modules in both slots (factory config), old 1GB module in lower slot and new 2GB module in upper slot, one new 2GB module in upper slot and empty lower slot.
At the same time Mini beeped/not booted in the following configs: 2 new 2GB modules in both slots (my target config), one new 2GB module in lower slot and empty upper slot and, most curios, one old 1GB module in lower slot and empty upper slot(!). The last one made me think bad of my brain, or eyes, or hands, or all at the same time. š
In search for solution I've googled "mac mini reset" and found this KB
http://support.apple.com/kb/ht3964. I tried resetting SMC as described in the article with 1GB module in lower slot and "Hurraa!" it booted, than replaced 1GŠ module in lower slot with 2GB and again it booted, finally added second 2GB in upper slot and my Mini also booted and showed me 4GBs of RAM in total.
Hope this helps to someone els!
Regards,
Petr