Random Slow Boot Times After Memory Upgrade?

I assembled a PC a year ago based around the Asus M4A87TDUSB3.0, with it was bundled a Phenon II X6 1090T and 2 x 2 GB fast DDR3. I have a 750W PSU, running a Radeon HD5570. I have a dual boot config, with Windows 7 64bit as default but also XP as other OS because there are some old games I really like that only work in XP (I tried emulation but software rendering isn't up to it). 90% of the time I'm in Windows 7. I've set up the system to that the Windows 7 partition isn't visible to XP, so that my Windows 7 restore points don't get wiped out when I boot into XP.Anyway, to cut a long story short, system has been working well, reliable and without issues for the last 10 months. However, a couple of months ago I decided to install a second drive of the same size but faster. I migrated the entire contents from the old drive to the new faster one without problems. I then reformatted the old drive and made it a dedicated backup drive for Genie Timeline. All worked well.

A couple of weeks later, I decided to upgrade the RAM from 4GB to 16GB and used Crucial's system scanner to find suitable upgrade. I took out the old modules, installed the 16GB new ones as a complete kit (with same latencies etc). First boot didn't seem to go well, system hanged before Windows Logo. I rebooted, went into BIOS and set the memory timings to Auto and set up Memory Counter to show on screen. I rebooted and it showed 16GB and it then booted into Windows normally. All fine, I did a Windows system rating and got 7.4's and 7.5's on everything apart from the HDD which comes in at 5.9Problem is, I now randomly get slow boots. It probably happens once in about 5 times, the entire boot sequence will take around 14 minutes whereas normally things are fine after about 3 minutes. I've pared down startup programs in MSconfig to really just the stuff I need to get by, so I know it's not that. If I shut down and restart, the chances are it boots fine again. It's not Windows Updates causing this, I can see those when that happens. I've taken out the memory modules and have cleaned the contacts with Servisol, unplugged and plugged the HDD connections back in. For a few days, the problem seemed to go away but it then came back.

When it's in its slow mode, everything is a bit sluggish, it's almost like I would imagine it would be with a minimum amount of memory or if it was running some heavy process in the background. I also notice when it's like this, that rather than the drive light being solidly on when booting, it's more of a fast flicker, with periods of inactivity lasting a few seconds.I'm not a technical expert, my guess is that it's either the hard drive or the memory. However, I'm also wondering if there is something in the BIOS that I need to do. Also, I've noticed that when shutting down, sometimes it doesn't quite feel like it's shutting down right, by this I mean that usually, in the last second before power off, the chassis fan runs to max as FanXpert hands control of the fans back to BIOS I guess