I just got my HD500 today and I found this while searching for "do this first" information:
http://line6.com/support/docs/DOC-2632

It describes your symptoms:

"...one of the tell-tale symptoms that may surface after a Monkey Flash Memory update is that the HD500 will be stuck in a continuous re-boot/power cycling state (you'll keep seeing the Logo and the unit keeps re-starting itself). Sometimes this may not occur, but a secondary telltale sign that a user has not performed a Global Settings reset is the USB communication between the HD500 and HD500 Edit software will be extremely slow/sluggish."

This happened to me a couple of times while I was using HD500 Edit and DAW Software at the same time where HD was looping during a boot up.  I resolved this by doing a global reset, see below.  This will erase all your customized/modified presets!  Hope this help!

On the POD HD500, you can reset the global setup options which includes resetting the Setlist names and pedal calibration by:

1. Disconnect the USB cable connection between HD500 and host computer.

2. Power off the POD HD500.

3. Power on the POD HD500 while holding the LEFT ARROW (<) button while plugging in the power supply to the POD.

***NOTE: Please also make sure to re-calibrate the onboard expression pedal of the HD500 after performing the Global Settings reset.

If the Onboard expression pedal of the POD HD500 does not sweep through parameter values as it normally would, you may need to perform a pedal calibration to reset the functionality of the expression pedal:

Re-calibrate the onboard expression pedal.

Hold the down the RIGHT ARROW button on the 4 Way Nav Pad while powering the unit on, until you see the “Test Mode” screen (Pedal Cal, etc.), and then proceed with the steps below:

1. If not already selected, use  on the 4 Way Nav Pad to select “Pedal Cal,” as shown above.
2. Press the VIEW button.
3. Set the pedal to the minimum “heel” position, then press the A footswitch to set a value for the Duty Cycle. You’ll see the value set to “100.”
4. Set the pedal to the maximum “toe” position, then press the B footswitch to set a value for the Duty Cycle. Again, you’ll see the value set to “100,” as in step 3.
5. Press the C footswitch to prepare for automatic selection of the Scaled Pedal Value and move the pedal from min. to max. You should see the Scaled Pedal Values read “0” at the heel position and “255” and the toe position. If you get values other than 0 and 255, power off and repeat these steps, starting at step 1.
6. Press the D footswitch to save the settings. You’ll be returned to the Test Mode screen and the Pedal Cal item will show a “P” to indicated that the pedal calibration is complete! Power your device off and back on again to start using it.