Missing recording sections

I’ve used Cubase LE 6 a number of times for recording but today something when wrong and I don’t know why.

The recorded tracks have sections missing. That is, while the recorded blocks appear continuous there are entire sections of recording missing (several minutes at a time).

I had only one inkling of this during the recording which is that the graph drawn on the track as it records was drawing an empty line sometimes. However throughout this time the levels on the input channels were going up and down normally. It’s as if Cubase just decided it wasn’t going to record for a while.

Has anybody else experienced anything like this?
Is it possible there are conflicting applications? The only audio application I can think I’ve installed since I last used this was iTunes, and that wasn’t running.

I’m running Cubase LE6 Version 6.0.3 Build 345.

Also - the day before I tested with the same equipment and recorded 1hr35mins continuously with no problems. The only difference today is that I wasn’t connected to the internet.