To my knowledge, main effects and interaction effects are independent of each other, meaning interaction effects will not have any influence on main effects and vice versa. Thus a significant main effect, as you describe, would not cause a spurious interaction effect.

If you have an interaction, one plan of action is to look at the simple effects to find out where the interaction is and work on your interpretation from there.

That does make sense. I guess I'm meant to consider that version itself does have an influence when considered with the variable time in that case.

It's just a little more confusing when the results generate significant interaction effects, but not significant main effects.

To re-affirm myself, significant interaction but no main effects would basically suggest that what is obvious, that when the variables are combined there is an effect, but stand alone there is none.

Guess I'll treat it as version does play a factor then (when we were hoping it wouldn't), and that I can't all the data into one group, even if version by itself is non significant.

Note that you're only going to have complete orthoganality if and only if you have equal sample sizes.

Had it not been for the version difference. My original sample size would have had a distribution of about 33 in one group and 37 in another group. (between-subjects).

Since there is an additional version difference.

I'll be forced to have more separate cells where some cells contain about 20 (Which sort of meets the recommended 20 samples per cell requirement) while others contain only 15. Unfortunately since it's not possible to get any more participants, I'm stuck with this data. I can't really tell whether this would be considered as unequal sample sizes in ANOVA, and I'm not sure what it's effects would be on additional research.

Hence my initial query about whether I should treat version has having an effect or not on the data.