After few days of testing.
I finally solved the problem of screen flickering ( when an app is opened, or few apps are opened), the screen will flicker on the app(s). This happened on Firefox, MS Word, Soundtrack (yes, I am still using it). iTunes, iPhoto, even "system preferences" etc etc.
First, my system was built via Time Machine restore - after SSD (Crucial 512Gb) on the SATA-3 port. ( theoretically would be slower compared to PCI-e SSD) on my 2014 Mac Mini 2.6Ghz, 8Gb memory. ( I chose the basic 2.6Ghz base model to save few $$, since I have two 512 Gb SSD laying around, instead of custom-build for 512 GB SSD PIC-e, with USD 1,299.00 price tag).
I tried numerous methods to avoid the flickering ie - PRAM reset, HDMI -> monitor, HDMI -> DVI cable, Thunderbolt -> DVI, Thunderbolt -> VGA on two different models of screen : no success.
The only time I could get a normal decent "flicker free" was when I booted into safe mode - after reboot - same issue.
I also used hardware check as Mini indicated "no issues" on the hardware.
I went to Apple Store and play with their set up - no issues (of course, Mac Mini was hooked on the Apple Display, wow!)
I started to wonder - either it would be OS X issues or "third party" software??
So, I took the 512 Gb SSD out (it is some sort of "pain" to open 2014 Mini), then used another SSD (120 Gb) for a clean install.
A fresh 10.10.1 on 2014 Mac Mini without other 3rd party software - worked great, no flickering at all.
I started to add the apps I normally have, one by one to test - UNTIL -- Microsoft Office 2011 (home and business version)
I have Outlook to synch with my Calendar, and typical Word, Excel, Powerpoint on my system.
As soon as I put Office 2011 on it - Voila! I found the culprit. It was running 14.4.6 version.
So, I put my 512Gb Crucial SSD back (another pain again) and booted up normally - same issues.
I have been check Apple to see if OS X 10.10.2 becomes general public release (hoping the problem would be accidentally fixed) - in the mean time, I was using my 2011 Mac Mini as the main system. 2014 Mac mini was on the disable list.
Until today, Office 2011 released 14.4.7 - I gave it a try and finally, Mac Mini 2014 with Iris GPU would not demonstrate "flickering" issues after the update!
Whew!!
Sam