If by "it loops the fill for the Main (A, B, C or D) I'm in instead, and continues to play", you mean that 'Ending1' plays a 'Fill' before playing the ending, and the style stops after the ending is finished, then this is how 'Ending1' works for any style on Tyros4, and as far as I know on all recent Yamaha arrangers.
It is not a problem with the styles. There is actually a Note about this at the bottom of page 48 of the 'Tyros4 Owner's Manual'!
Note:
If you press the ENDING/rit. button
when the Style is playing, a fill-in automatically
plays before the ENDING/rit.
'Ending2' and 3 do not do this unless you press the 'Fill' button first.
However for all 3 endings, the style should stop after the ending pattern has finished.
If you want to use 'Ending1' but avoid the fill, just copy 'Ending1' to 'Ending2' or 3 using Style Creator's 'Assembly' function.
Regards
Ian