It may not be a problem. There is no rule that they should be the same brightness; in some presets only one LED should be working.
To check the function of the remote, try using the Miscellaneous\Signal Test preset - with this one you should see both LEDs on and the same.
For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=9&t=7356#
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