Exactly the same for me, and today (one day after I flashed CWM) my phone has these bugs all the time+another bug, the browser lags, and is extremely slow(scrolling).
I tried serveral logcat apps and nothing..
You can do this if you enable TDB funcion in CWM. The diffeence about MIUI stock with ROM's from this site (MIUI Android) is that they removed all the things that come from Xiaomi wich will be useless like Store, Weather and other things to chinese market, fix GPS outside china. If I'm not mistaken they only make this to developer ROM's not in the JLB.
If you still have problems, lkie I've said try to stay with mimimum things and backups, to help isolate the problem.
Since i flashed JLB17 trough fastboot i cant restore the backup i made. Now i have to do everything again and chinese pops up everywhere i think i am going to full wipe everything again. And just install a rom from MIUIandroid from a few weeks ago. See if the problem still exists
Also there is chinese on my spashscreen now :S
Also a little bug facebook chat heads are not working :S even when i turn it on in settings.
Edit: Fastboot flashed an older version the spash screen is back to normal
That's why I said that backups aren't the best idea... When you switch from one system to other may have bugs that isn't on the system, but in your backups. The logcat is helpful to developers related to Xiaomi team, you could sent a report trought the app with the description.
I just wiped everything flashed latest rom and restored my backup. I noticed that most of the problem began after using fb.
So i gave it all permissions under settings > all settings > apps. I tikked everything on yes for fb and fb chat. Now the catheads work and i get notifications normally + my buttons didnt dissapear so far if the problem comes back i will go to the JBL you gave in the link