I may be able to help you as I have a JVM410H and modfactor, timefactor and space in its loop.
JVM's channel volumes act as send levels on the fx loop and especially when in +4db mode they are pretty hot when channel volumes are above 5 (noon) causing the eventides even in line mode to clip and thus to sound "weird".
The solution is to use them in -10db in fx loop, guitar level in eventide (i don't know if there is a switch in H9) and channel level in 5 (noon) so that the input level eventide sees is optimal (in eventides meter is at about 70% and does not clip even with the hottest guitar pickups as Anderson h3+).
It is a well documented "feature" of the JVM and if you go to JVMforum you wiil see more examples with other pedals, and even many pro rack systems, that have the same problem.
Hope i helped!