Can you please provide more information for us to try to help you figure out what is happening?
Your computer specs and such (look at my profile signature at the bottom of this post of mine, to get an idea of the info that folks find helpful)
Also, what about settings, like the 'Prepare Using' parameter - (Cakewalk folks set it to a new default of 250, down from its original 500 setting. Sometimes, setting that back to 500/750/1000 solves some dropped notes issues. (worth a shot anyways). Sorry I don't remember the full name of the parameter in preferences - I have been up all night recording, and I have to get 45 minutes of sleep prior to heading off to rehearsal for Mother's Day service at my church. (playing piano/keys for it).
Driver Mode?
What sort of audio interface do you use?
Anything you can think of to supply us, will hopefully help your issues get resolved.
Bob Bone