The order of the pubkeys given in addmultisigaddress affects the generated multisigaddress.
Consider non-multisig-addresses A and B with pubkeys pA and pB then
addmultisigaddress 2 [pA,pB] and addmultisigaddress 2 [pB,pA] generate two different addresses.
(I have tested it only with two addresses)
If this is intended then nevermind. But it was quite an error hunt today to find out...