Can you disable on-board cache from BIOS? Given that the K6-2+ has on-die L2 cache, the motherboard's cache gets to be L3 cache - might confuse Win98?

If i disable the onboard cache it boots and seems to work ok. How do i go about getting it working with the motherboard cache enabled, does it require a reinstall of Windows? What's the impact of the running with the motherboard cache disabled.

I have the same SS7 board, among others. P5BB0103.BIN should be the latest BIOS.
I'm currently running a K6-2+ 550 MHz on it (overclocked to 600 MHz) and I don't have any issues. The system is very stable with or without active MB cache. Now, for what it's worth, motherboard cache is not really needed for the K6-2/3+ CPUs, since they all have full speed L2 on-die cache (so the improvement with the MB cache activated is marginal).
Anyway, what I would try:
1. make sure you are indeed running the latest BIOS
2. check that, in fact, the DIP switches are correctly set (FSB 100 MHz, multiplier, vcore voltage). Also make sure that RAM is set to run at FSB speed, not AGP speed.
3. do a CMOS reset
4. remove any peripherals while doing tests (I had some strange issues with this board/CPU together with a USB 2.0 PCI card)
5. If you have other memory modules, see if the behavior is any different with them (FYI, I'm running one 128 MB PC133 memory module, I feel that going for 256 or more is completely overkill for SS7).

Thanks for the info but still no joy yet, i get Windows protection errors now on boot.

1.) Checked the BIOS, i was running a different version. It had a later date but i've flashed to the version you mentioned but it's made no difference.
2.) I've checked the dip switches for a K6-2+ 450mhz with 2.0v i have it set to 0001110000. Changed RAM to run at FSB speed, it was set to run at AGP speed.
3.) I've Reset CMOS.
4.) I've removed everything but the AGP card for now just to do some testing, still the same.
5.) I had 3 x Memory modules installed 2 x 32Mb and 1 x 64Mb. I've removed two so that i just have the single stick of 64Mb.

I've also tried to install a clean Win98 on a spare HDD to see if that makes any difference but it doesnt, the machine works fine booting from floppy, partitioning and formating drive then going through the install process until it get to the detecting devices stage then freezes.

Yeah, the issues during the "detecting devices" stage are a clear sign of instability (either caused by memory, overclocking, etc). Back in the day, this was the first stability test that I would try: installing Win 98 from scratch.
Are the board's capacitors in good shape? I know you said that before changing the CPU it was working fine, however it's hard to say what the behavior might be with a different CPU. According to this, the typical power consumption for the K6-2+ 450MHz is a bit higher than that of the K6-2 300 MHz, so if your board has some issues (leaking/bulging capacitors near the VRM?), this might just be the final push over the edge.

Of course, there's also the possibility that you have a bad CPU (either damaged in some weird way, or requiring more voltage in order to run properly at its nominal frequency - something that was a bit too common for the old K6-2 CPUs, but not that common for the K6-2+ CPUs). So I would also try giving the CPU 2.1V or even 2.2V, just to test - don't worry, if you keep it cool, it can handle it without a problem.

I've had a quick look at the capacitors but they look fine, I've just switched to a new corsair power supply to see if was the power supply but its exactly the same. I've also upped it to 2.1v but it still wont boot with the motherboard cache enabled, i had a quick look on ebay at getting another super socket 7 motherboard but wow the prices have shot up. A decent one costs more than a brand new motherboard! I might look to re cap it anyway i have a de soldering station and i'm not to bad with the soldering iron so figure it wont hurt, just need to get the right capacitors. Thanks for you help and suggestions.