I'm going through this process as well, but I'm having a much different experience.
I recently got married (Feb. 2012) and moved provinces so I submitted both an address change and a marital status change form, along with a letter stating my husband's world income for 2010 and 2011 to the office in Winnipeg. The main difference from the others here is that my spouse is here on a working holiday visa, which is really just an open work permit, and so he had a temporary SIN number. We're still in the first stages of PR application.
In any case, I had forgotten to include his date of arrival in Canada in my letter, but I received a personal phone call from the person responsible for my file. She asked for the date, informed me that my spouse had to file taxes for 2011 for the portion of time he was in Canada (even though he was not working) and that would be that. She said if he didn't, when the next (July 2012) GST payment is scheduled, the system will attempt to cross-reference my file with his for the calculations and if his file is not there, the payments will be stalled.
In the mean time, I just received an additional payment for the GST and provincial credit that was owed to me for the time since I married since our joint income was still below the income threshold. So. So far so good. I expect a delay in future payments because his taxes were submitted late, but otherwise, I've been impressed with the way it's gone...
The main difference I see between those having troubles and mine is that my spouse had a SIN number and our combined income was below the appropriate threshold so I didn't have to pay anything back....also I went through the Winnipeg office...