By the way. if you're using R4 version 1.1, make sure you get it to 1.11 first. if you made a typo mistake. you can consider my suggestion below.
Eventhough i don't know how to fix your problem. I can tell you R4 with firmware 1.11 should work with dragon quest monsters joker. just need to find a way to fix this problem. If i found a problem like this, i think the first thing I'll do is 'format' the sd card and re-install the firmware directly from the R4 website and try again. My sister also have a R4 (same as me). I've never encounter a problem yet. but she did a couple of time. Eventhough i don't understand the exact problem, i always just do this for her first and the problem is fix. I tested her R4 with my SD card on my DS for a couple of weeks and is fine. then i tested out her SD Card with my R4. ran into problem. so i am sure that's what happen for the last couple of time. SD card problem. she replaced the SD and ever since. no problem.
so after this long story. if you don't know what's going on yet, just try formating the SD and re-install the firmware flash from R4 website first. at least is clean and eliminate all the other possibility first. Since this rom is working for most others, this will eliminate most software problem first. (also if the ROM is downloaded here, where everyone got it from) then you can start eliminating problem by asking a friend to test out with their SD or R4 or their DS. it may surprised you by using this elimination, you'll find out your problem very quickly.
PS. i basically finished the game and i got my rom from dash. (i think is the same one romulation put up, since the file construct is the same) not sure if i am supposed to post this. but you can google it. it is working perfectly.