User extensions not showing up on phones

what exactly is the phone model?
It sounds like a limitation that is imposed by RC provisioning server.

I am going to give you an example with a random phone: Yealink T42

T42 supports up to 15 line keys. And if you take a look at the pic below, you’ll see that it has 3 pages, 5 line keys per page, the 6th line key is used to go to the next page.
 

If T42 is configured on RC however it only has up to 6 line keys - that’s because the 6th line keys is replaced with a normal line key, so you are no longer able to go to the next page. Not only that but RC also enforces the first 2 line keys to be your own lines, leaving you with 4 line keys to configure for other extensions.

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You said 3 out of 12 are not showing. 
Therefore I assume your phone has 9 line keys per page - and the 10th key is used to go to the next page.
However RC config has overwritten this for you - so you have a user extension on line key 10 instead of the button to go to next page. 
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So how to solve this? 4 options:
1. Manually provision the phone. 
PROS - it’s free
CONS - you’ll have to set up line keys and all functions directly on the phone - the admin portal will stop reflecting changes to the phone. For example things like Presence/Call pick up will have to be configured manually on the phone.

2. Custom config - you’d have to reach out to RC since only they can apply a custom config. Custom configs work by overwriting the default config you get from RC provisioning servers.
PROS - you’ll be able to set presence on the admin portal
CONS - RC will most likely charge you for a custom config
CONS2 - not all phone models support custom configs (hence I asked at the beginning what model phone you got?)

3. Key templates might help if your phone model is supported(hence I asked what model phone you got?). - this would allow you to reassign the first 2 line keys which are normally reserved for your own extension. i.e. you can think of this as getting 2 extra line keys.

4. Leave it as is
Not really a solution.