Dan has said for years that he feels that daily shaving tends to work best for acne prone skin and you need to be sure you are shaving with the hair and not against it. If the acne flared up when you started growing your beard, this is probably because as you said you couldn't apply bp through the beard. Now that you have been shaving again, make sure of your technique. Watch Dan's videos. http://www.acne.org/faq.html#shave and http://www.acne.org/...to-shaving.html
Since your beard area does better when you shave regularly, you may just have to continue with shaving. Get back strictly on the regimen and the breakouts there should get back under control.
Hope that helps.