Hey I just jailbreaked my iPhone 3GS 3.1.2 with blackra1n
and I installed backgrounder because I want to run some apps in the background.
but it wont work, neither will winterboard.
Winterboard wont even start and backgrounder doesnt show the message "Backgrounder is enabled" when i hold down the Home-button, it just returns to the home menu..
Is there some known problems with this or is it just my phone?

you are going to want to jailbreak with an pwned ipsw from the new PwnageTool the dev team released today. geohots jailbreaks come out quicker but arent fully refined and are generally missing some pieces to get things like winterboard and generally anything that requires MobileSubstrate to work properly.

I'm running 3.1.2 with a blackra1n jailbreak and Winterboard and Mobile Substrate seem to be working fine -- the only 'gotcha' I'm aware of with blackra1n is that it doesn't register the afc2 root service during the jailbreak so you need to do it manually if you want root filesystem access with the USB utilities. More info (and fix) for that issue is available here:

Issue 153 - iphonebrowser - 3.1.2 Jailbreak Issue - Project Hosting on Google Code

Are there other issues in relation to the blackra1n jailbreak that would affect Mobile Substrate and Winterboard that I'm not aware of? The afc2 service should only impact ifunbox and iPhoneBrowser, or DiskAid, etc., from my understanding.

EDIT: Reader's digest condensed version of the fix: You can manually edit your .plist file and reboot OR you can download afc2add from Cydia (which I have done and worked with no problems).