That is an IR remote so let's look at potential issues.

Does the original remote work the sub correctly?

Make sure when learning codes to your remote, you follow these tips:
     a) Make sure to use 'new' batteries in the transmitting remote.
     b) Keep the remotes spaced between 6" to 12" apart. Make sure you have them facing the correct way.
     c) Make sure there are no stray light sources from fluorescent, sunlight, or other broadband light sources. This could include a laptop screen. If unsure, use a blanket to cover over the remotes when you learn (make sure not to block the area in-between the remotes).
     d) When learning, start with the push & hold method. Press the button for 2 full seconds that you want to learn. Next try feathering, rapidly tap the button while it's learning.

The software usually tells you when you have learned a good code. What does it say when you try to learn a code into the software?