Audio Glitching Randomly

Hi -
I'm having an issue whereby (seemingly randomly) the audio on my machine starts glitching and stuttering - sometimes it's more like popping / clipping noises (but very intrusive) and other times it sound like there's an echo which repeats very briefly everything in the audio, which comes across like a stuttering effect.
It happens in iTunes, Quicktime Player, VLC, youtube, previewing audio in Finder etc 
The only place this doesn't happen at all (which is pretty fortunate) is Logic X - which always behaves totally fine - I assume this could be a clue for someone that may point to the issue?! Funnily enough in looking at an old session on Logic 9, it does do the stuttering there....
I'm using an Apogee Duet audio interface, all the drivers are up to date, as is all the software on the Mac.
I'm not sure what triggers the issue, but frequency-wise it may happen 4 times during a movie - and it then irons itself out and is totally fine...(but during the melt down it's unbearable!)
Any help at all would be very gratefully received, I have to find a way to fix this issue!
I've seen similar posts on other forums, but no solutions....
Thanks,
Mike
Apogee Duet Audio Interface
MacBook Pro
OS X 10.9.2
2.7 GHz Intel Core I7
16GB Ram 1600 MHz DDR3

Thanks very much for looking into this!
I don't have any antivirus sodtware, and definitely not MacKeeper!
Here's the results from EtreCheck:
Hardware Information:
          MacBook Pro (Retina, 15-inch, Early 2013)
          MacBook Pro - model: MacBookPro10,1
          1 2.7 GHz Intel Core i7 CPU: 4 cores
          16 GB RAM
Video Information:
          Intel HD Graphics 4000 - VRAM: 1024 MB
          NVIDIA GeForce GT 650M - VRAM: 1024 MB
System Software:
          OS X 10.9.2 (13C64) - Uptime: 0 days 11:58:52
Disk Information:
          APPLE SSD SD512E disk0 : (500.28 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 499.42 GB (296.7 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
USB Information:
          LaCie Rugged USB3-FW 500.11 GB
                    EFI (disk1s1) <not mounted>: 209.7 MB
                    External MBP Samples (disk1s2) /Volumes/External MBP Samples: 499.76 GB (90.16 GB free)
          GenesysLogic USB3.0 Hub
                    GenesysLogic USB3.0 Hub
                              Seagate  Expansion Desk 3 TB
                                        EFI (disk2s1) <not mounted>: 314.6 MB
                                        Studio Backup (disk2s2) <not mounted>: 3 TB
                              GenesysLogic USB3.0 Hub
                                        Seagate  Expansion Desk 2 TB
                                                  EFI (disk4s1) <not mounted>: 209.7 MB
                                                  Media Drive (disk4s2) /Volumes/Media Drive: 2 TB (1.68 TB free)
                                        Seagate  Expansion Desk 2 TB
                                                  EFI (disk3s1) <not mounted>: 209.7 MB
                                                  Project Drive (disk3s2) /Volumes/Project Drive: 2 TB (1.65 TB free)
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Inc. BRCM20702 Hub
                    Apple Inc. Bluetooth USB Host Controller
          GenesysLogic USB2.0 Hub
                    Kensington      Kensington Expert Mouse
                    GenesysLogic USB2.0 Hub
                              Apple, Inc. Keyboard Hub
                                        iLok iLok
                                        Syncrosoft eLicenser
                                        Apple, Inc Apple Keyboard
                              GenesysLogic USB2.0 Hub
                                        M-Audio USB Keystation 88es
FireWire Information:
          Apogee Electronics Duet 400mbit - 400mbit max
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
                    Apple Inc. Thunderbolt to FireWire Adapter
Kernel Extensions:
          com.Apogee.driver.DuetFWOverideDriver          (1.4.4 - SDK 10.8)
          com.kensington.trackballworks.driver          (1.1.1 - SDK 10.6)
          com.paceap.kext.pacesupport.snowleopard          (5.9 - SDK 10.6)
Launch Daemons:
          [System] com.bombich.ccc.plist 3rd-Party support link
          [System] com.bombich.ccc.scheduledtask.31C0605B-8B80-4281-B6A1-ED85D66DB25F.plist 3rd-Party support link
          [System] com.bombich.ccc.scheduledtask.6F09CEA5-1C03-47B8-8CF6-7E1FF4E3AF43.plist 3rd-Party support link
          [System] com.bombich.ccc.scheduledtask.D6537BFE-DBEA-4B0D-AE30-0BFC3E3E24CC.plist 3rd-Party support link
          [System] com.bombich.ccc.scheduledtask.EF91FE58-ED1A-45A9-A3B2-88A3D3C32E87.plist 3rd-Party support link
          [System] com.DuetDaemon.plist 3rd-Party support link
          [System] com.paceap.eden.licensed.plist 3rd-Party support link
          [System] PACESupport.plist 3rd-Party support link
Launch Agents:
          [System] com.ApogeePopup.plist 3rd-Party support link
          [System] com.eastwest.server.plist 3rd-Party support link
User Launch Agents:
          [not loaded] com.bombich.ccc-user-agent.plist 3rd-Party support link
          [not loaded] com.google.keystone.agent.plist 3rd-Party support link
          [not loaded] com.spotify.webhelper.plist 3rd-Party support link
User Login Items:
          iTunesHelper
          Dropbox
          Google Chrome
          TrackballWorksHelper
          Logic Pro X
Internet Plug-ins:
          LogMeIn: Version: 1.0.935 - SDK 10.7 3rd-Party support link
          LogMeInSafari32: Version: 1.0.935 - SDK 10.7 3rd-Party support link
          QuickTime Plugin: Version: 7.7.3
          Default Browser: Version: 537 - SDK 10.9
Safari Extensions:
          Searchme: Version: 1.2
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
3rd Party Preference Panes:
          TrackballWorks  3rd-Party support link
Old Applications:
          /Applications/Euphonix
                    MC_Client:          Version: 2.7.1.88549 "" - SDK 10.5 3rd-Party support link
                    Uninstall EuControl:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    EuControl:          Version: 2.7.1 - SDK 10.5 3rd-Party support link
          MemServerUI:          Version: 1.1 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/Native Instruments/Kontakt 5/kxm/MemServerUI.app
          /Library/Application Support/PACE Anti-Piracy
                    iLok Client Helper:          Version: 3.6 - SDK 10.5 3rd-Party support link
                    InterLok Helper:          Version: 5.9 - SDK 10.4 3rd-Party support link
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Equalizer/AuthAssistant.app
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Exciter/AuthAssistant.app
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Dynamics/AuthAssistant.app
          licenseDaemon:          Version: 1.3 - SDK 10.5 3rd-Party support link
                    /Library/PrivilegedHelperTools/licenseDaemon.app
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Imager/AuthAssistant.app
          DC1A:          Version: 1.2.1 - SDK 10.5 3rd-Party support link
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Maximizer/AuthAssistant.app
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Reverb/AuthAssistant.app
          AuthAssistant:          Version: 1.0 - SDK 10.5 3rd-Party support link
                    /Library/Application Support/iZotope/Ozone 5/AuthAssistants/Main/AuthAssistant.app
Time Machine:
          Skip System Files: NO
          Auto backup: YES
          Volumes being backed up:
                    Macintosh HD: Disk size: 465.12 GB Disk used: 188.80 GB
                    External MBP Samples: Disk size: 465.44 GB Disk used: 381.47 GB
          Destinations:
                    Transcend [Local] (Last used)
                    Total size: 931.19 GB
                    Total number of backups: 2
                    Oldest backup: 2013-03-20 07:10:20 +0000
                    Last backup: 2013-11-04 18:05:18 +0000
                    Size of backup disk: Too small
                              Backup size 931.19 GB < (Disk used 570.27 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               6%          Google Chrome
               4%          WindowServer
               1%          EtreCheck
               0%          Dropbox
               0%          fontd
Top Processes by Memory:
          279 MB          com.apple.IconServicesAgent
          246 MB          mds_stores
          197 MB          Dock
          131 MB          WindowServer
          131 MB          Google Chrome
Virtual Memory Information:
          11.30 GB          Free RAM
          2.77 GB          Active RAM
          702 MB          Inactive RAM
          1.23 GB          Wired RAM
          827 MB          Page-ins
          0 B          Page-outs

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