Could a few people please run this special build? It'll amnesty the dust spam transactions, which will clear up the 0/unconfirmed problem for now. We really just need one block letting them through to clear up the previous transactions. Post if you generate a block with this.
These are binaries only. The linux version is 64-bit only.
SHA1 fb7c66270281ed058c570627cf7baff0bdc16e5d bitcoin-0.3.13.1-specialbuild-win32.zip
SHA1 9fc44ea5f2109618073e2cfd887e2cc266eb31a9 bitcoin-0.3.13.1-specialbuild-linux64.tar.gz
The linux 64-bit version includes a change to the cpuid 4-way 128-bit SSE2 autodetect for AMD in 64-bit mode, if you'd like to test that and see if that's better.