I forwarded your question on to one of our support people, and he said the wiring scheme on the H3000s is different, which may be contributing to the problem. See below. He recommended doing a factory reset, then just connecting it by itself to see if it works.
Connection and Level Guidelines for XLR and ¼" Jacks
High Level Signals ALWAYS Use the XLR Connectors
Many Eventide audio products give you a choice of XLR or 1/4" input and output connectors. When a +4dB line level signal is fed to an Eventide from a +4db FX Loop Send/Line Out/Preamp Out, you must use XLR connectors for inputs and outputs on any Eventide unit. This is true for: H3000/3500 DSP4000/4500/4000B GTR4000 DSP7000/7500/4000B+ ORVILLE/ORVILLE R ECLIPSE H8000/H8000A
The H3000/3500 only have XLR connectors, and these can be changed to accept either +4dBm or -10dBm nominal operating levels. They are set to "pro audio," +4dBm at the factory. To change this, remove the top cover of the unit, pull the small jumper blocks from the +4 pins and put them on the -10 pins. Refer to the H3000/3500 manual for a detailed schematic. Warning : disconnect MAINS before opening the unit. Refer to a qualified technician if in doubt.
DSP4000/4500/4000B/GTR4000/ECLIPSE handle unbalanced -10dB signals on ¼" input and output connectors.
DSP4000B+/7000/7500/ORVILLE/H8000/H8000A handle unbalanced -10dB signals on ¼" input jack connectors. There are no ¼" output connectors, so unbalancing of XLR outputs is required. This is described below.
Use line level cables (2 connectors + Ground) as those made by pro audio companies like Mogami, Belden , Canare, Monster Cables, Klotz, etc.
Input from unbalanced ¼" jack: Connect XLR Pins #1 & #2 to ¼" Ground Connect XLR Pin #3 to ¼" Tip
Output to unbalanced ¼" jack: Connect XLR Pin #1 to ¼" Ground Leave XLR Pin #2 unconnected Connect XLR Pin #3 to ¼" Tip
Use line levels cables (2 connectors + Ground) as those made by pro audio companies like Mogami, Belden, Canare, Monster Cables, Klotz, etc. Always keep balanced the cables ends connected to the Eventide XLRs I/O and unbalance the ¼" ends connected to unbalanced gear.
Input from unbalanced ¼" jack: Connect XLR Pins #1 & #3 to ¼" Ground Connect XLR Pin #2 to ¼" Tip
Output to unbalanced ¼" jack: Connect XLR Pin #1 to ¼" Ground Connect XLR Pin #2 to ¼" Tip. Leave XLR Pin #3 unconnected