What color timing marks do you have choosen and have you used that color to place timing marks.
I have discovered this weekend that it's MUCH more responsive to the proper timing marks if you choose a color that there are NONE in your sequence at all. Baring that from working, changing the active color of timing marks you are "viewing" and then changing it back sometimes works too.
I do exit the program every 30 minutes or so and re-load and that fixes some odd timing issues too. it's almost like it get's "lost" in them.
BTW make sure you draw all your elements before you start trying to sequence. A couple of help fellows over at the LSP forum has finally drilled it into my head that LSP is smart enough to know DOWN on an arch will naturally start in the middle.