Good day, KnightofChivalry,
Yours is a problem not often encountered, and, to be honest, the rarity of this sort of thing (the portrait problem) happening surprised me. So, what I did is I opened up my NewGen Editor and decided to try out a few things to help me truly understand and, hopefully, uncover a solution in the process.
Unfortunately, I could find no direct solution, but that is primarily because I do not know what you have in your map.
Could you perhaps post a beta, openable version of it here? Or could you perhaps elaborate? Please be more specific.
An off-hand guess would be that your units are using custom models, or that perhaps you're initiating some GUI/Jass command that effects the unit's appearance. If you do have a custom model, try making sure that they are all pathed to the correct custom path (the correct path is usually posted on the same webpage on the model download) in the Import Manager (F12). If you are changing the unit's appearance via triggers in the game, then perhaps try making a new unit with the Object Editor (F6) with the exact same appearance that the unit would look like after tweaking it and use the "Unit - Replace" GUI command in a cinematic "cleanup" trigger to replace the manipulated unit with its new look-alike unit.
However, these are merely guesses - if they aren't your answers, please either post a few screenshots, post a beta version of your map or just tell us more about your problem.
As for your sky problem, this is one of the problems that some beginners encounter. Sometimes people create a sky in the editor through the "Map Preferences" options under the "Scenario" menu. If you did this in hopes of it appearing in-game, then it is WRONG! This is what you should do:
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Sky Init
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Events
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-------- This example will be using Map Init --------
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Map Initialization
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Conditions
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Actions
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Environment - Set sky to <YourSkyType(E.g"Felwood")> Sky
If you're already doing that, then it's likely that you're using some imported texture as your sky. Check its pathing in the Import Manager (F12)
I hope this helped
