Could you please clarify your questions a bit?
1. What do you mean by “accurate result”? When you run many realizations, you can get the output for individual realizations either in the charts or when you export the data. Typically when we run the model we run for at least 40 MC realizations and look at the average, or median and at the 95% MC confidence intervals.
2. There are several possible reasons why your results don’t match your input targets: it could be that there is not enough area available for the transition (in this case not enough area would transition), it could also be some kind of a configuration error (for example in a spatial run transition targets must apply to individual types and/or transition simulation groups). If you want to send me your library I could take a look and see what the reason is specifically in your case.