Are you perhaps using Fences?

If you are using Fences 1 on Windows 8 then the icons will never show without a right click.

If you are using Fences 2.x on Windows 8 then the icons will appear, but depending on what icons are on the desktop and what else is loading, it can take 30-60 seconds before they appear.  A right click hurries this along.  This is because Fences sets the icons to hidden until it is loaded.

Start8 itself should not be having any impact on this other than getting you to the desktop quicker which could make you notice the Fences slowness more.

Fences 1 has never worked correctly on Windows 8.  The system it uses to autoload was broken by Microsoft and this is why without a right click it will not show the desktop icons.  This happens with or without Start8 and if it was working before I can only imagine some app was triggering the right click logic in explorer and so causing Fences to run the init code.

Oh, yeah... right clicking doesn't help; they're just GONE; system icons AND shortcuts.

Well, things got worse with Fences 1 installed...recent updates to the Windows OS (8.1) rendered Fences effectively useless as one could not add icons, move icons, or pretty much do anything other than open the program/docs associated with the icons that existed before the update occurred. In addition, none of my desktop icons could be moved nor could I add any new ones.

I uninstalled Fences 1 and was able to again move my desktop icons and add new shortcuts to the desktop.

I subsequently installed Fences 2 and its capability was again restored.

It appears the opportunity to run a free version of Fences is a thing of the past.

I only wish Fences was reasonably priced. I am a paid user of Start8 and would consider paying a similar amount for Fences 2. $10 is comparatively quite extreme when one takes actual functionality into account.

Hopefully Stardock might reconsider its pricing strategy for this add-on.