Why does all video stutter on playback?

Please forgive the long post. I wanted to be thorough.

This is my first Mac. I've just got a new (refurbed) "Late 2012" Mac Mini to replace a 2007 Windows Media Center PC from Acer (specs of both below). The old Acer would play video fine if it wasn't doing anything else. On the Mac, I've tried playing video from various formats and sources, and all of them appear to have low frame rates (they're not smooth) and video played from files appear interlaced. The result is adequate playback where there is slow or no movement, and horrible jolty, interlaced playback when people move, scenes move or there is action. Here's what I've played:

• BBC iPlayer streamed online
• YouTube
• 720p MKV files from the local hard drive in VLC
• 720p MKV files from the network (both over gigabit ethernet with CAT6 cabling and WiFi) in VLC
• Live TV through an Elgato Diversity and EyeTV software
• Live TV through an Elgato Diversity in Windows Media Center in Parallels (running Windows 7 Ultimate 64-bit using Windows Basic colour scheme)
• Live TV through an Elgato Diversity in Windows Media Center in VMware Fusion (running Windows 7 Ultimate 64-bit using Windows Basic colour scheme)
• Recorded TV through an Elgato Diversity in Windows Media Center in Parallels (running Windows 7 Ultimate 64-bit using Windows Basic colour scheme)
• Recorded TV through an Elgato Diversity in Windows Media Center in VMware Fusion (running Windows 7 Ultimate 64-bit using Windows Basic colour scheme)

With the exception of the EyeTV software, I was previously able to run all of these in Windows on a six year old PC, which has considerably a lower specification.

Mac Mini specs:

• OS X Mountain Lion 10.8.2
• 2.3 GHz quad-core i7
• 16 GB 1600MHz DDR3 SDRAM (Crucial)
• 1 TB 5400 RPM SATA hard drive
• Onboard Intel HD4000 graphics
• Elgato Diversity dual digital tuner
• Output to a TV via HDMI using 1280 x 720p @ 50 Hz
• Connected to either;
  • WiFi 802.11n 5 GHz AirPort Extreme
  • Gigabit Ethernet via CAT6 cabling to AirPort Extreme
• I don't think any other specs will be relevant

For reference, the previous Acer Aspire iDEA 510 specs:

• Windows 7 Ultimate 32-bit

  Using Windows Aero

• 1.66 GHz Core 2 Duo T5500
• 2 GB 667 MHz DDR2 SDRAM (Crucial)
• 2 TB Samsung HD203WI 5400 RPM SATA hard drive
• GeForce 7600 graphics
• Integrated hybrid dual digital/analogue tuner
• Output to a TV via HDMI using 1920 x 1080p @ 50 Hz
• Connected to Gigabit Ethernet via CAT6 cabling to AirPort Extreme

The reason for the question is that this Mac Mini was chosen as a more than capable replacement as a media PC, and I had initially hoped that video performance of Windows 7 in Parallels or VMware Fusion would be sufficient to watch live or recorded TV. However the interlacing and lower than expected frame rate doesn't just affect video in a VM, but everything I play, from any source via any medium.

Odd? Before we delve into checking error logs and hardware problems - which I'm not experienced with on a Mac - can I run my two initial considerations for the culprit by you:

1. Mountain Lion 10.8.2 - I have read there could be issues with this release that were not present in 10.8.0 or 10.8.1. Should I wait for 10.8.3 to see if any potential video playback issues are fixed?
2. Intel HD4000 graphics - Perhaps this isn't up to the job of playing video. But I wouldn't expect it to have a problem with YouTube, and though I haven't checked the benchmarks, surely it must outperform a 6 year old GeForce 7600 mobile chipset?

Finally, I am yet to try Windows 7 via BootCamp. I will do, and will report the results. My suspicion is that it should play adequately, as it all did previously, however I am particularly loathed to count this as a "solution", as I would lose the ability to use OS X. Otherwise I could've just bought a Windows PC. And I didn't. Nor do I want to.

Some other things I have yet to test: determining the actual frame rates in VLC (for example) on both the Mac and old Windows PC. Also, streaming YouTube from an iOS device to OS X using AirServer or similar to see if I experience the same issue. I suspect I would.

Does anybody have any suggestions? If you would like me to check anything, instructions for dummies would be handy.

Thanks in anticipation!

Al