Why are there differences in exon naming for some transcripts/genes?

Two different conventions are used for exon naming.
Systematic Exon Numbering starts at 1 and counts and numbers each exon numerically. So, if there are 10 exons, for example, they will be numbered from 1 to 10.
Whereas Custom Exon Numbering is the historical numbering that was determined when the gene was first sequenced. The Custom Exon Numbering originally included splicing variants. For example, if there was a splicing difference, you could have an exon numbered 10a in one transcript and 10b in another transcript. With Systemic Exon Numbering, this exon would just be numbered 10 if it was the 10th exon. The Custom Exon Numbering usually comes from the original paper and/or the scientist that determined the sequence. This had previously been supported by NCBI but was discontinued several years ago in favor of Systematic Exon Numbering. However, researchers still use Custom Exon Numbering for genes such as BRCA1 and BRCA2.
In the AlamutTM Visual Plus toolbar, if you click on “Exon Naming” you can change between the two naming conventions. Alternatively, you can set the program to “use systematic exon numbering by default”. To do this, open the “Alamut Visual Plus” menu > “Preferences”, and then select this setting in the “View” tab.