Fitting Gaussian to data: Density-Estimation vs Regression
The difference comes about because the sample mean and sd estimators are assuming the data is a random sample from the distribution on the full range of the distribution, in this case -Inf to +Inf. In your second case above there's no data below zero. The sample mean estimator can't see that you've only got half a Gaussian there, it will always be a positive number.

On the other hand, the curve-fitting approach of the least-squares fitting procedure (which is presumably possible via EM, or any of a dozen other algorithms) can see the data as part of a curve that has a Gaussian density shape. If the data is just curving upwards, it will fit to the left side of a Gaussian. If its curving down it will fit to the right side. If its flat it will either fit it to the peak with a very large variance, or a tail and might even go degenerate and divide by zero.

So you are doing parametric estimation of a distribution, or curve-fitting, which are categorically different things.