You have to set the Master checkbox to apply the effect to the whole track. Did you forget to do that?

I sorta figured out what was causing this but it brings up another issue that wasn't present in the old versions...

if I assign chorus to an instrument (I assigned to instrument 20) and echo to a channel (I assigned to channel 31), they seem to cancel each other out if instrument 20 is in channel 31!!! in previous versions of ModPlug it would just use Chorus and Echo together... it won't do that in this new version...

You're seeing again issues that don't exist. Yes, this happened exactly the same way in the old versions. Instrument plugins always override channel plugins. If you want the instrument to also be routed through the echo, you will have to select the Echo from the Chorus plugin's "output to" list. For this to work, the Echo plugin must be in a higher FX slot than the Chous plugin.