This is going to sound dumb, but the first thing you should do is make sure you have really fresh batteries in your remote. Sony remotes seem to be especially persnickety that way.
Once you put your Sony into standby, if you reboot, it remembers it was in standby and goes back into that mode, so simply rebooting will not help. I'm searching the archives to see if there was an answer to your question.
I found a thread in the archive
where TCF forum member stevel posted a file to program a Pronto remote to act like the Sony remote:
Originally Posted by stevel
If you get a programmable universal remote, such as Philips Pronto, you can program a button to send the "Standby" code. All TiVos accept such a code (different for Sony and non-Sony models), but only the Sony remote has a button for it.
For Pronto users, I have the Sony standalone remote codes (and a CCF) on my web site
The server load protection has kicked in, so I can't get to the other threads in the archive I wanted to look at, but try putting in new batteries and see if they will help.
A recent test showed that the new Energizer e2 batteries outperformed all other batteries by a whopping margin for devices like digital cameras, PDAs, and other electronic devices like that, so I'm going to be switching to those for my remotes the next time I change the batteries out.
Hope this helps.