Lost vs fixed population
I am not sure I understand your question. It seems to be a matter of definition. The term lost and fixed populations sounds quite wrong. I have never used PopG. Is the PopG manual using these terms without defining them?
Probability of loss and probability of fixation
Given your parameters, you will clearly expect that, if fixation occurs, then it is as likely that the allele a fixes than the allele A fixes. In other words, the probability of loss and the probability of fixation for a neutral locus are equal if you start at frequency 0.5.
Did you say recessive allele
Note that there is no recessive allele at least in terms of fitness (but you probably don't have an explicit phenotype that is afterward link to these fitness values anyway) in your simulation as all genotypes have the same fitness.
Extra info: $F_{ST}$
If I understand your parameters correctly, you are simulation an island model with constant migration between any two populations with D=100 populations. In such circumstances, the $F_{ST}$ should be $$F_{ST}=\frac{1}{1+4N(m+\mu)\left(\frac{D}{D-1}\right)^2}$$ which is approximatively equal to $\frac{1}{1+4Nm}$, where $m$ and $\mu$ are the migration and mutation rate respectively.
Because of migration, you wouldn't expect that all population would be fixed for one or another allele at any time point.