If both systems are not each exactly 90 deg to the RA axis then they are non-orthogonal. This means that each imaging system will scribe a slightly different arc through each exposure even though the guiding system is working fine. I'm no mathematician but i remember doing some work with Gary Kopf at Astrofest one year trialing an AN update and it was one of the things we were working on modelling. I'm sure he would know more about it (as I'm sure plenty of others here would as well) so maybe drop him a pm?
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