Equity Risk Model Using PCA

I'm trying to build a simple risk model for stocks using PCA. I've noticed that when my dimensions are larger than the number of observations (for example 1000 stocks but only 250 days of returns), then the resulting transformed return series (returns rotated by eigenvectors or factor returns) have non-zero correlation.

Intuitively, I can see why this might be, since in the pca process I am estimating a 1000x1000 covariance matrix from 250x1000 observations. So it is like an underdetermined system. But I'm not exactly sure what's going on. Can someone explain what is happening?

Also, for risk model purposes, is it better to assume a diagonal covariance matrix or use the sample covariance of the factors?

Here is some matlab code to demonstrate the problem:

% More observation than dimensions
Nstock = 10;
Nobs = 11;
obs = randn(Nobs, Nstock);
rot = princomp(obs);
rotobs = obs * rot;
corr(rotobs) % off diagonals are all zero

% More dimensions that observations
Nstock = 10;
Nobs = 9;
obs = randn(Nobs, Nstock);
rot = princomp(obs);
rotobs = obs * rot;
corr(rotobs) % some off diagonals are non-zero