Is this only happening when you make changes to service request?
As far as I know, some changes on the front end, i.e. request offerings do not get added to the project. There is a separate option for pushing those changes in the OPS console. I haven't tested this yet to see how exactly it works but I'm guessing it just replaces your request offerings with the source.
I have version 2016.1.1 and don't believe I have those options but it is not an issue of applying the package, It is an issue with the transactions not applying to custom project. For ex, If I make a change while Project A (custom project) is selected, the transactions are applied to the Default project. Once I move the transactions to Project A from the Default project and assigning a package it is applied to UAT successfully.