The short answer is No, one should be fine. :)
Most motherboards that support double and triple channel configurations don't require it; you just don't gain the performance of the feature if not using the right configuration (ie: three matching sticks in the right slots).
So I dug through the Supermicro C7X58 manual to ensure that standard is in use and it appears it is (P. 2-10 - "Population Recommendation"):
"Performance: Install one DIMM in slot DIMM1A (the first slot in Bank1), OR one DIMM each in slot DIMM1A and DIMM2A (the first two slots of Bank1)."
Your problem seems to lie in your RAM - you state "the RAM chip is ECC/Registred", but the specs for the motherboard state you need Non-buffered RAM ('buffered' = 'regsitered'):
"1600 / 1333 / 1066 / 800MHz Un-Buffered ECC / non-ECC DDR3 SDRAM 72-bit, 240-pin gold-plated DIMMs"
You should check over their Supported Memory List for that board (it's a link off the Specs. page linked above) to ensure you are getting/using compatible RAM.