Hi hadikhan64, I and TyrusX had a discussions several pages back regarding precisely this matter. A couple of weeks ago, a visa officer from the Detroit office came to the University of Waterloo and held a question and answer session regarding permanent residency.
Several students were wondering whether or not research assistantship experience that is remunerated through incomes that come under T4As rather than T4s can be counted for immigration purposes. To sum up her response, she basically said that the students should be able to document job responsibilities, and estimated number of hours in their letters of references, and submit any relevant T4 and T4A forms with their applications. She added a caveat though, that the amount of financial support should cover the period in which the students are working. For example, if you claim 40 hours a week, and the wage per hour turns out to be, say, something like 2 bucks an hour, then it might have raised some concerns.
My interpretation of her response (actually, I've had this interpretation even before she came to our campus) is, since RA/TA is classified under NOC 4012, which is considered skill level A, then provided that your financial assistance covers the number of hours you claim as work experience, and the salary per hour works out to be above the minimum wage, then it should be fine. Besides, there is no limit for the number of hours international students can work ON-campus (which is the case for RA/TA experience, or any work done under study permit [rather than off-campus work permit which imposes the 20-hour per week limit]).
HOWEVER, since you are applying under the PhD stream, it might not be wise to claim full-time work experience during the period that you are also claiming to be doing PhD full-time. Remember that the definition of full-time study is 15 hour per week, so it may be okay to claim something like 20 - 25 hours a week, but anything above that would be pushing it. In fact, that was probably why they were crediting your credit card back (since the studying full-time towards PhD part is an integral requirement for this stream).
Also, since we're not really sure if this is going to work yet (our interpretation of "paid work experience" can only go so far, and in the end, it will all depend on the visa officers evaluating our cases), then it's probably better if you had actually included the letters for the other work experience you had. I suppose only time will tell how it's going to go. Please do let us know what happens as this will be a very crucial information that may be useful to a lot of other people trying to apply under this stream
Anyway, can you tell us about the timeline of your application?