Note:  If you have version 5.0.0 or later of BioEdit, there is a chance that your preferences file has 'N' missing from its list of valid amino acids.  Also, if you want characters such as 'X', 'B' and 'Z' to be included in similarity/ID calculations, those may need to be added to the list as well.
If it is missing, it will cause errors in similarity/ID shading of protein alignments.  To put the 'N' back in where it's supposed to be, either download and install the
In addition, 'U' may be missing from the nucleic acids list, depending on when the program was downloaded and if your preferences were overwritten.
new BioEdit version from the full installation, or follow the instructions below:

1.  Open "Options->Preferences" and click the "General" tab.
2.  On the right side, under the "Amino Acids" or "Nucleic Acids" list, locate any characters you want included in an ID/similarity calculation in the "Don't Include" list, then highlight them and click the '<' button to move them over to the 'Include' list.
3.  Press "Save & Close"

If you want to be safe, and just have all cahracters counted, just highlight everything and move it to the "Include" list.
There is an option in 5.0.8 or later to either count non-included characters as positions or ignore them completely when doing similarity/ID shading.  It is found on the same preferences page as the include lists.

Sorry about the bug.