This is part of why it is not officially supported.

Not officially supported, eh?
http://www.dosbox.com/comp_list.php?showID=3120&letter=W

That list is done by users, not the DOSBox team.

Windows 9x (unlike 3.x) is an OS in itself. It comes with its own low-level DOS modules. Therefore, there is no need and it makes little sense to try to install it inside DOSBOX, which emulates DOS. It is easy to believe there can be many different conflicts and issues leading to what you experienced.

If you want Windows 95, installing it inside a PC only emulator (not PC + DOS which is what DOSBOX is), is probably your best bet. Microsoft Virtual PC is one such emulator.

Gives it an windows protection error when rebooting?

Can you boot into Safe Mode?

The only thing you need win95 in dosbox is to run win95 3DFX games.

For applications or 2D games better use another emulator.
VirtualPC, vmware, virtualbox, etc...

It gives a BSOD.

Try truth5678's guide for Win95b installation in DOSBox.

In general, for ykhwong's build you need:

In DOSBox type: imgmake с:\hdd.img -t hd_2gig. This will create 2 Gb fat16 HDD image.
In dosbox.conf input:
machine=svga_s3, vmemsize=4, memsize=128, core=dynamic, cputype=pentium, cycles=max, isapnpbios=false
in [ide, primary], [ide, secondary], [ide, tertiary], [ide, quaternary] enable=true;
in [autoexec]:
imgmount a "c:\fddboot.ima"
imgmount c "c:\hdd.img" -t hdd -fs fat -ide 1m
imgmount d "c:\win95.iso" -fs iso -ide 2m
boot -l a
(fddboot.ima for example you may get in [boot] folder of .iso Win9x CD after opening it by 7zip)
Run DOSBox. Run setup from CD image. After setup change to "boot -l c".

Some had problems with Microsoft's S3 driver during setup. You may need to choose VGA there. Then you'll set recommended S3 drivers from DosFreak's guide, DirectX 8.0a, driver for SB16 and Voodoo. For some games other video driver may be better, for example some VBE. SB settings in Device Manager should be manualy set to 220 7 1 5.

collector wrote:

This is part of why it is not officially supported.

It's supported unofficially. And on practical side DOSBox works not bad in ykhwong's port for many Win9x games. Anyway, it's general discussion section but not developers official help thread.
Even Direct3D 5.x games may be played, but this needs ~3 times faster CPU cores for good fps than we have today or better support of 3D cards in the emulator.

It's Dosbox genersl discussion, Dosbox does not support it. Topic closed.
Ask ykhwong directly or follow any of those guides.