After some testing i found something that works for now.
I added this
numf.RefreshDisplay = MoveAndResizeDivAndAddFlash;
to the StyleInputFileAndAddFlash(inputFile) function
from this threadmodified the MoveAndResizeDivAndAddFlash() function
from
height = replacementDiv.style.height = replacementDiv.offsetHeight + "px";
to
height = replacementDiv.style.height;
as replacementDiv.offsetHeight was always returning 0 after displaying the hidden div
I left the width line the same as it would return a proper value.
In my client side code after I display the div i call the RefreashDisplay function and it works properly.
NeatUploadMultiFile.prototype.Controls['ctl00_ContentPlaceHolder1_inputFileId'].RefreshDisplay();