I have a Logitech Harmony One, and it works great so I'm sure the 900 will work for you as they are basically the same remote with the 900 adding the RF functionality.
I basically adjusted the "Power On Delay", currently I'm using 13000 and it seems to be working well for me.
To make this adjustment, add your MRX as a device on the Logitec Harmony and...
Step 0) Log into your Logitech Harmony Remote Software
Step 1) Select the "Devices" tab in the Harmony configuration home screen.
Step 2) Find the MRX in your list of devices
Step 3) Press the "Settings" button
Step 4) On the "Device Options" screen, select 'Adjust the delays (speed settings)' and press the "Next" button
Step 5) On the "My AV Receiver takes the following times to respond to commands" screen, adjust the "Power On Delay" to '13000' and press the "Next" button
Step 6) Finish the adjustment configuration wizzard and update your remote with the new timing settings.
Please see the attached screen shots that highlight the steps listed above