The Legacy Mode is not related to this issue. It really is only there so you can continue to run old, unsupported software that uses Martin Kahr's driver internals dependent Apple Remote code, which has been broken once again by the new OS X Apple Remote driver in 10.6.2.

Today, however, pretty much every serious, supported application (including XBMC, Plex, Boxee, EyeTV, ..) using the Apple Remote uses my HIDRemote class - which doesn't have any such driver dependencies and therefore also doesn't need the Apple Remote driver to emulate the internals of old driver versions from previous OS versions.

Given your description, your problem probably is a battery that's about to run empty. In that case, the Apple Remote starts sending extra IR codes with every button press, which may explain your issues. Normally, OS X (or Remote Buddy) will inform you about a low battery. Since that battery warning, however, is also sent as a HID event, that HID event is only received by the application that currently uses the Apple Remote (and there usually can only be one at a time) and most applications don't implement any warning when receiving a low battery HID event, chances are you'll never see any warning come up.

My recommendation: try with a new battery.

Best regards, 
Felix Schwarz

P.S.: RowMote, just like Remote Buddy's AJAX Remote, uses Wi-Fi as its communication channel, which is far more reliable in transmitting information than the IR technology the Apple Remote uses.