While I appreciate replacing a soldered in battery with a battery holder, you have ultimately replaced the battery with a non-standard part.
the battery you replaced had 2 solder connections on one side, and one solder connection on the other.
on the side that has 2 solder connections, you must utilize BOTH holes. you have to tie them together with a wire, as each through hole is used for different parts of the board. if you only use one, it wont work as the battery must supply voltage to both of them to properly work.