No problems; how are you comparing the variables? There are limitations on how the comparison expressions can be implemented.
There is an open issue to modify the blocks so it won't be possible to make expressions that aren't supported by bBasic: https://github.com/haroldo-ok/vcs-game-maker/issues/12
Unfortunately, until those guardrails are implemented, you would need to be careful to only use simple comparisons and avoid mixing `AND` with `OR` on the same expression: https://www.randomterrain.com/atari-2600-memories-batari-basic-commands.html#if
Anyway, could you please show an screen capture of the expression that is causing problems?