Sometimes these issues can be rectified by checking all your cables, especially the white coaxial are snug and tight.
Virgin's channels are carried in groups of clusters, and the 2 you refer to are in the same cluster so it sounds like the agent was probably telling the truth.
Here is a picture showing the channels in that cluster that should be affected.
Sign into Check Service Status at the top of this page. It shows any local faults, and may show yours, plus the estimated fix date and time.
More importantly you can also run a test against the set top box. By doing this VM should be able to try and connect to your box and determine what the problem is. Sometimes this results in them sending out a replacement and/or engineer, which saves a phone call.
If nothing is showing you could also try the Service Status number 0800 561 0061. This often gives details of more local issues down to postcode level.
.If the above doesn't help then you should call 150 from a Virgin landline, or 0345 454 1111, option 2 (Faults) butbest to call between 8am and 10am to avoid call queues, or late afternoon around tea time
When calling Faults hopefully the system will recognise that you've used the online faults checker and place you into a queue for an agent to pick up.
If not and you get the automated response asking you to press 1 for the link to online support etc, ignore all the options and don't press any buttons then you should be placed into a queue and an agent should pick up the phone and resolve the problem.
The Service you do for others is the rent you pay for your room here on Earth - Muhammad Ali