I had mentioned this before under the 'FILL delay post', but here goes ...
Some of the delays you 'might' be experiencing in some of the styles could be indeed due to any of the reasons you've already listed above. In the SD1/X units, I do believe though that the GROOVES do have a part to play with what might seem to be a delay when in transit from a FILL to A, B, C or D. For the most part, in order to avoid such, most of the FILLS have been programmed to carry forth the groove used in the previous ARRANGER part. Eg the DRUM2/GROOVE track of FILL_1 will utilize the groove/drum2 used in ARRANGEMENT_A. In cases where these vary, you might notice a slight 'glitch' as you go from FILL -> ARRGR. Since they are LIVE-DRUMS, they really cannot accurately be QUANTIZED because that will then defeat the purpose and eliminate a lot of that 'human' aspect. (Quantization of DRUM2 is possible).
A way to reduce this effect would be to turn OFF the AUTO-CRASH. This way, you'll experience a 'smoother' transistion b/w fills and other arranger parts, the reason being that the AUTOCRASH is programmed right on the note (1/4, 2/4, 3/4 etc) and dis-abling it enables you to smoothly go from the grooves used in the FILL to the grooves used in the ARRGR, since they are all grooves. Should you be using eg a LATIN rhythem that's made up of mostly GROOVES (which are not strictly QUANTIZED), there could be a 'clash' in transition when using AUTOCRASH (since the Grooves anre NOT quantized exactly on the notes and the AUTOCRASH is). Hope this helps ... at least from an understanding point as to why.