"Just recently I did a fresh installation of Mavericks 10.9.2 onto a new Samsung 840 EVO 250GB SSD (connected via an ICY Dock Enclosure) and placed it into my Mac Pro 4,1 (2009) 8 core as my main system drive and have since been experiencing strange Fan behaviour.

When I boot my Mac up everyday for the first time the Fans run at full speed, but if I reboot the problem goes away?
(Were any errors logged at startup? (console/log errors, anything not initializing at startup, etc.) After a reboot does fan rpm always stay low? (If not, does Temperature Monitor ever show any high sensor readings?)
If you don't reboot after a cold start, do the fans stay at max rpm? (failsafe mode perhaps?) How long have you waited to see if they eventually reduce in speed? Just curious.)

I have tried resetting the SMC and PRAM but it still happens.
(Do you have another boot volume? If so, is it always OK booting from another Disk? (or a boot in safe mode).)

I have also recently added a UAD-2 Quad PCIe card as well as replacing the stock graphics cards (GT120's) with an ATI Radeon 5770 which was a while ago.
(Were the UAD-2 PCIe DSP Accelerator Cards installed (and OK) before the SSD upgrade? (i.e. was the only change before fan problem appeared just the SSD.) If not, does removing the UAD cards change this behavior? (TS by simplifying the equation so to speak.))

This is the first time I have experienced odd Fan behavior since purchasing the Mac 5 years ago."

I don't post there so the above are just some ideas off the top of my head. (Maybe someone sharper than myself can reply with other/better suggestions.)
  

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