peterNH - Let's skip to the chase. Move the curser to the beginning on the project. Arm a track for record, hit RECORD. If you have the metronome set for a precount of one bar, you will hear four beeps (4/4 time) and then the recording will begin as the curser begins to move.
What do you have there? If the recording starts immediately, you have not setup the precount.
Cubase 6.5 (6.5.5) and 5.5 (5.5.3), WaveLab Elements 8, iC Pro remote app, LoopMash HD, Win7 64-bit, Intel C2Q9550@2.83GHz, 8G ram, Radeon HD 6570, Gigabyte X48-DS5 MB, Mackie 1640i (FireWire), M-Audio Keystation 61es controller via an M-Audio Midi-Sport 1X1.