When saving a Signature configuration document, the esig.nsf database re-saves the configuration document to convert the Rich Text to MIME/HTML.
This HTML is then used when the email received at the server is in a MIME Format.
The signature is appended directly after the last line of the e-mail and it has always been the responsibility of the signature creator to add the number of Carriage Returns required.
In Lotus Notes 8.5 this conversion has changed slightly resulting in inconsistent < br > tags. When saving the Signature configuration you should use 'soft' carriage returns. i.e. insert a '[shift] [return]'. This will correctly generate the correct number of < br > tags.