My girlfriend and I filed our 2008 taxes jointly. We don't have and don't want a jointchecking account. We used the "free notary service" offered by my bank, whereby the branch assistant manager notarized a durable power of attorney giving me authority, by my girlfriend, with regards to any and all matters of state and federal income tax filing, payments, etc., and specifically the authority "to endorse and deposit or cash 2008 federal and state income tax returns".
There are a couple of things wrong with your scenario. First, you have referred to your girlfriend, and not to your wife. The IRS does not knowingly allow unmarried individuals to file joint tax returns. If you represented yourselves as married in order to file jointly and you are not married, you could be charged with tax fraud.
Secondly, refund checks issued by the IRS for joint returns are always issued with the joint payees joined with an ampersand ("&") which makes them payable not alternatively. Finally, your bank is not compelled to accept any check for deposit, and it may refuse the IRS check for any reason, your power of attorney notwithstanding. A small claims case would probably not result in recovery of any fees.
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