I also played with Tilted Twister. As I understood your problem, your TT never solved the cube correctly. To solve the cube there are two important issues where TT is not 100% reliable.
1. read colors
NXT 2.0 color sensor is very good in recognizing basic lego colors as red, yellow, blue, green ... but colors on the standard rubik cube are different.
usually TT has problems to recognize between dark red and bright orange.
Try to run TT in dark.
my experience is that TT sometimes doesnt flip the cube successfully. One wrong move in a sequence will never finish with solved cube.
I made some improvement in a construction and in the code. I got success rate 1:3 but never managed 100%. They are described in my posthttps://sourceforge.net/apps/phpbb/mindboards/viewtopic.php?f=4&t=72#p1910