I agree...I've been getting this with every plane since I first installed the sim...just turn off "Aircraft Stress", and forget about it.
I really don't know why you should be having this problem. I've never experienced this phenomenon in FS9 or any other version of FS/CFS.
One possible explanation for some 3rd party aircraft. I've not experienced it with default aircraft & I should point out that this is not as common in FS9 as it used to be in earlier versions of FS. Some 3rd party CFS aircraft will literally blow up when they first load.
If an aircraft appears to "drop" when it first loads in the sim, go to Spot View & press the Y key. This will put you in Slew Mode. Now press Y again to show why this is happening. To correct it experiment with the static_pitch = & static_cg_height = entries in Aircraft.cfg. These entries define the static ground position of the aircraft in Slew mode. Here's an example of what I mean.
Slew Mode

Normal flight mode.

It took me a while to find this example & although it drops a couple of virtual feet this is not enough to damage the nose or main gear legs on full realism settings. Nor is it affected by toggling the views.