Troubles with Drivers and question about arduino IDE cache

Hi, im facing since i m on the 1.6.x IDE series very strange behaviours

I m on W7 familial edition, on a Aspire TimelineX (2012)

I m facing since the 1.6.x series very painfull troubles in uploading sketch (not possible) or discussing in usb serial with the arduino.

I m using essentialy jeenodes v6 and jeelink classic, wich are UNO type: http://www.digitalsmarties.net/products/jeenode

Those troubles happended 3 times in the last 3 months: february, march, and just today.

The trouble ( not being able to load a sketch, or communication in serial being trunkanated way arduino to computer) happens suddendly, and with scripts that are working
.

I precise that my scripts are not changed before the problem occurs, and are not part of the solution.

There seems to be a kind of instability due to following things:

-windows update. Arduino is seen on its COM port, but cant be loaded. Its not a trouble of Selection of com port, nor Arduino family type ( i m on 2009 and UNO bootloaders)

-USB 2 or USB3: communication (receiving in serial at 14400 from arduino to computer) doesnt no more work for me if i m on a USB2 port. It works on the USB 3. I was incriminating the drivers of my usb ports, but a friend of me encounters 10 days ago the same problem: Jeelink can work for him only on USB2, computer (Thinkpad w520) just having been up to date . Wich is for the USB part exactly the contrary of my experience.

-it happened also for me with UNO RC3, making me loosing 2 complete days around the code, wich was not the problem/ I had to do all the update asked by windows ( i was late of one or two update, wich is quite nothing).

-IDE change: Today i was stuck by the suddednly impossibility to upload my sketch.
Two days ago the 1.6.4 IDE said to me a new version was around.
Blocked, without any windows update to do, i finally decided to download the 1.6.5.
And there, i can upload correctly is now working.

So, my question is very simple: i m now suspecting the IDE itself.
Why would the upload fails with the 1.6.4 suddendly and works with the 1.6.5 ?
Is there a CACHE, some file to be cleaned ?

What is your opinon about those weird troubles ?

I can accept its a matter of drivers, or different causes together, but actually i m widely developping a project for this year around arduino, and passing times and doubts about the code where the trouble is elsewhere is not possible.

Other question is:
Is there another way to upload sketches than the Processing IDE ? Sounds there is really a leak somewhere.

anybody around ?