not all games work particularly well on the r4ds such as the pokemon black/white gen. << they need patches.
after searching i dont think there is a patch for this game. i would get banned if i were to tell you where to get a rom. but it is either something to do with compatibility on the r4 gbc emulator (use lameboy), something
in-game for whatever reason, a glitch, or the classic bad rom (pretty sure its that).
DONT GIVE UP, i had loads of issues with r4ds compatibility but i managed to figure them all out via google or trial and error. just remember if switching roms you can use the same .sav file u already had. im sure you knew that already but anywayyyyy... good luck
there are lots of bad roms out there cloned from website to website. it might take a while to find a good one.
(i and emulator-zone are in no way endorsing illegal downloading of roms)
EDIT: Ok its definately the rom you have, according to another thread on this forum, some revisions of this game had room errors and all search around for the
missing mushroom thread here somewhere for the same game. he got a newer revision and said the mushroom appeared. so ya, you just need a newer revision of the rom.