It was inevitable, so here we go. While fixing my broken random encounter patch, I discovered a little bug with Random Number Good: overworld encounters are not using Think's RNG. What should have been a call to the RNG to determine whether an encounter should be triggered, is instead a static number, causing overworld encounters to happen with astounding regularity. I forgot how the vanilla RNG worked; it does in fact return a different number each time, but it's using a tainted version of vanilla's RNG system (since Think's code overwrites part of the random number table vanilla used). It may still be random "enough" for encounter purposes, but it's not what it should be.
The fix is just one byte long, but I'll let think share an updated version of the patch here for inclusion in the next point release. I'll instead share a set of updated patches for the random encounter mod, with the fix baked in, so that it can be properly tested this time.
Patches (updated to v4)
Apply directly to your 1.9.
EDIT: With Nowea's help, I re-jiggered some numbers and also went ahead and applied the encounter mod to the overworld as well. This should have the effect of setting the minimum number of steps before an encounter to 9 in dungeons and 5 on the overworld (excepting high encounter areas like forests and WoR deserts). Obviously, this will also fix the faulty overworld encounter logic, so you should notice a difference in overall encounter rate there (increased, according to Mishrak). Dungeon encounter rates should remain the same.