Thanks for your help on this Ernie.
I thought you'd like to know that I also found another, more permanent solution, that eliminates the need to juggle with the route and 'Build from waypoint' option.
Somewhere in your paperwork you mentioned that the program uses the first intersection listed in the fsb_int.txt when there are two or more with the same name. I found that if I put the Paphos intesection first in the text file the program built the route correctly each time.
Surprisingly I had hit the same problem on the very next route I tried to build from EGKK to LEMG when FSBuild used D070K BKY070011 (near EGLL) instead of D070K MID070011 (near EGKK). I tried the same solution by putting the MID intersection first in fsb_int.txt and , hey-presto, it works correctly every time.
If you build flight plans from or to the same area(s)/airport(s) fairly often this solution should give a fairly permanent fix.
Best regards
Graham
