Also, if you are running a 4.5.xxx OS, it's possible that you have entries in multiple calendars on your Blackberry. The today themes only look at one, which could explain the missing entries.
When you open the calendar app, are the text/backgrounds for the 'missing' items the same as for the ones that show up on the today screen? The 4.5.xxx calendars are color coded - one for each email address that you have set up on your phone.
For more info and steps to correct, go
here.