I've seen our CRJ Collins FMS produce that message for a variety of reasons.
(Bare in mind FMS on CRJ-200 is older than FMS-6000 I believe)
1) Unable what is set as cruise in PERF INIT because the VNAV planned will not let you reach CRZ ALT before reaching another altitude constraint you put in the LEGS page whether it be on the way up or on the way down. Sometime putting the ILS on a short flight which brings with it the fixes with their altitude constraints will produce an "UNABLE CRZ ALTITUDE" msg.
2) YES, It seems FMS tables are different in many aspects from the books. Seems like it interpolates more than the tables did. Flex temp would be a good example of that.
3) I've seen it come before with no rhyme or reason, a couple times it seemed like temp affected it tho not sure what was so unusual that day.