Why does my MacBook Pro close open programmes when it sleeps?

Hi,
I'm having an Auto Sleep issue with my MacBook Pro (13 inch, Mid-2012).
When my mac goes to sleep it closes any and all open programmes. Not only is this annoying but it means the mac can't be left to run a process, such as a length Time Machine back-up, as it will close down the programme mid way through.
The issue happens when running on battery or mains power.
I've gone to System Preferences > Energy Saver > and I've set the Computer Sleep slider-bar to be Never.
I've done this for both Battery and Power Adaptor settings.
I've also made sure the 'Put Hard Disc to Sleep when possible' setting is disabled
I've tried changing to these Power Saver settings then restarting immediately but no joy.
It only seems to happen when the mac goes to sleep from inactivity. If I manually put the mac to sleep it doesn't happen.
It hasn't always done this. It started about a year after I purchased the Mac (new from Apple).
I recently upgraded to OS X Yosemite 10.10.1. and this hasn't done anything to fix it.
I've tried searching the net and various Mac forums and I can't seem to find anyone reporting the exact same issue. I'm hoping someone on here will be able to help.
Any ideas anyone?

Or take it to your nearest Genius Bar; if there is a problem, you can exchange it for another machine. Or return this one (14 days from the date of purchase if it was purchased from Apple) and buy another.

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Model Information:
Serial Number:          9G02903MAD3NB
Manufacturer:          DP
Device Name:          bq20z451
Pack Lot Code:          0
PCB Lot Code:          0
Firmware Version:          201
Hardware Revision:          2
Cell Revision:          164
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Charge Remaining (mAh):          509
Fully Charged:          No
Charging:          Yes
Full Charge Capacity (mAh):          5066
Health Information:
Cycle Count:          450
Condition:          Normal
Battery Installed:          Yes
Amperage (mA):          -742
Voltage (mV):          10807
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