Have you tried new batteries in the new remote? (it's amazing how often new remotes still need them replacing)
Did you use the codes detailed in the /Downloads/VM%20TiVo%20TV%20Remote%20Code%20List%2012_11.pdf list? Sometimes more than one code works so don't just accept the first one that appears to work, try a few more.
Press and hold down clear and TV at the same time, until the light on the top of the remote flashes green twice. Then enter the four digit code for your TV’s make and model number from the list. The LED should then flash green twice.
Then press Vol +/- and Mute to check that the remote is working. If not, repeat the steps above using a different code for your TV from the list. Once programmed the light on the top will flash green instead of red when using it for Standby, Volume and Mute control.
The same applies if you use the '999' method, don't just accept the first one that appears to work.
Searching for a TV remote control code using 999
Press and hold down clear and TV at the same time until the light on the top of the remote flashes green twice. Then enter the code 0999 to access the TV code database – the LED will flash green twice.
Press channel up until a code turns off the TV – the LED will flash green each time a code is sent. Once the TV turns off, release channel up and press standby on the remote to turn the TV back on.
Press vol +/- and mute to check that the remote is working with your TV. If they don’t, continue to search using channel up until the next code turns off the TV, and repeat steps 4 and 5. When the Volume and Mute keys work, press OK to store the code. The LED will then flash green twice.
(If you reach the end of the code database, the light on top of the remote will give an extended red flash and exit programming mode)