Very often, some of the frequencies on the license will either be devoted to conventional, or held in reserve and inactive as the system grows. The other possibility is that the other 2 are strictly "goto" frequencies when the normal home channel is busy. When a particular channel is busy, the LTR controller will send traffic to the active home channels you have already found, and very rarely to the "missing" frequencies. In this case, you need to be monitoring during the day, which are business hours, and keep checking. If they are being used, you will have to be patient waiting for them to show up. I have one system where the same home channel is used as "goto" 90% of the time. This is not typical of the 7 other systems run by the same outfit, so there are so many exceptions you will go nuts,
IF you find conversations cut off, you may have a bigger problem. Often, system operators will use frequencies from another license at another location, or maybe the same location. Check the FCC database for different locations by the same FRN number.
The HP-1 needs to be added to this, but some of the principles will be the same.
Mapping an LTR System BTW, do you have the extreme upgrade?