This can always happen to such a complex numerical like ENVI-met. We have invested a lot of time to increase the internal intelligence of ENVI-met. The recent version can handle a lot of trouble situations by itself and find a solution to ensure a proper model run. However, sometimes things simply don't work, and here are some clues what to do:

• Don't be sad or frustrated! Remember that you are working with a complex numerical model. 10 years ago this had required a million euros super-computer. Only because the computer you use was much cheaper, that does not mean that the program has become easier to handle. It's the other way round.
• Try to extend your model area via “Nesting Cells” if your have trouble with the flow.
• Move complex buildings away from the model border.
• Extend the vertical extension of the model.
• Decrease the time step if the model gets unstable in the normal calculation loop. (See [TIMESTEPS]-Section of the manual)
• Consider simplifying your model. It's not the real world either, so you can adjust some very complex corners to an easier configuration

Also have a look at the warnings and information in the ENVI-met program output. If your model is not working, send the input files (.in and .cf) to me! I love to receive mails and also it helps to find bugs and improve the program!