Many issues after upgrade to 8.8.6 + Patch

[Labsy]

Hi,

I am kinda flooding the forum, but hopefully under this topic it seems more promising. Many simmilar issues.
So I'll accumulate my issues so far:

1.) I did first MIGRATE from old Ubuntu 12.04 to 14.04. Copied over to new Ubuntu box whole /op/zimbra, then MySQL and matched all passwords and mailboxes on new box.
This worked.

2.) then I upgraded ZCS on new box from 8.0.9 to 8.8.6
Also this upgrade went pretty smooth, if I don't count some prerequisutes which need to be installed on new box.

3.) WORKED FINE, except some Windows XP users were not able to connect anymore (due to fresh SSL certificate probably).

4.) Then after almost 1 week I begun getting complaints:

SOME users were not able to connect, regardless of their computer OS and Outlook version.
Found out some having SPACE after username (weird...where did it came from?)
The rest of problematic can retreive mail SOMETIMES, and SOMETIMES they don't. Might be 3 days OK, then 1 day not.
I get a lot of these errors in /opt/zimbra/log/nginx.log
SSL_write failed SSL: 32: Broken pipe while proxying
viewtopic.php?f=15&t=63658

Also, configured EXTERNAL accounts IMAP retreival inside Webmail failed for ALL users.
Here's thread on this issue, only IMAP problems, POP3 works fine, no hints yet:
viewtopic.php?f=15&t=63705

And another weird thing, which might be just my lack of knowledge is:
lsof command returns tens of thousands of open files, like in this post:
viewtopic.php?f=15&t=63711

Any ideas appreciated.