I seem to have encountered a bug when using both a Custom Lineage and a Custom Background. I created the Custom Lineage first and then the Custom Background and everything worked fine. However, I went back and changed the config on the background and all of the proficiencies & languages disappeared from my character sheet. If I switched to a standard background it worked fine, but if I switched back to custom background nothing showed up no matter what changes I made. I then tried switching to a standard race and as soon as I did, the custom background proficiencies & languages showed back up. In order to make sure it wasn't a one-time glitch, I switched back to the custom lineage and the custom background still worked. However, as soon as I changed anything on the custom background, the proficiencies & languages disappeared again.

If the proficiencies from a Custom Background do not show on the character sheet - this is usually because of a caching issue. It will often fix itself after about 20 minutes - though it could take longer - especially recently.