So I got a new wii updated it and got some homebrew apps and when I run them the player 2 remote just blinks.
Is there anything im doing?
Is it system 4.2U(SA)?

What apps?

uhh games like super mario war and Still alive wii and other apps that have multiplayer.
I just connect them both and whem i get into the HBC poof p2 is dissconected.

Okay, try not connecting the 2nd wiimote, and only try connecting after the game is launched. Does it work now?

I've never had any problems playing multiplayer on SMW before....

Also, make sure the batteries are fresh. :P

Uhh what do I click to get it conected after the game starts? 1 and 2?

I'd assume so...

didnt work :( should I try again?
the p2 remote just flashes blue

Try resyncing it:

Press and hold the red button under the SD card flap on the wii and the red button under the battery pack on the wiimote for 15-20 seconds. Then try connecting in SMW.

This is getting frustrating im already getting mad.
Is this a system 4.2 thing?

I used to be able to and the i update HBC to the 1.0.4 and it no longer works...I don't know if that had anything to do with it but it was around the same time, it worked before and it doesnt work now.