Lower E super overpowers other strings on looper, but sounds normal on amp?

Like the title says, when I connect my guitar to my looper and play the individual strings, the low E string is super loud while the higher strings are barely audible. However if I connect directly to the amp, this isn’t an issue and all the strings are at a similar volume. I’m still a beginner so not sure what the issue could be, any advice would be appreciated!

The guitar is a Martin 000-X1ae, the looper is RC-1 and the amp is a Cort AF30 if that helps? The guitar has a Fishman Sonitone pick up and it’s located at the top of the sound hole, closer to the lower E string. I was thinking that might be the issue, but not sure as there’s no problem when I’m plugged straight into the amp?