\include "paperXX.ly" was deprecated in the 2.3 branch in favour of the #(set-global-staff-size XX) idiom and is no longer accepted by Lilypond.
Using #(set-global-staff-size 26) in version 2.8.7-2 does not seem to cause the problem described in this bug. I have attached a simple 1010-bar piece that shows no collision with bar numbers with three (or even four) digits. Unless this is just my configuration, this bug can now be closed. Regards, -- Chris Lamb, Cambridgeshire, UK GPG: 0x634F9A20
186124.ly
Description: Binary data
signature.asc
Description: PGP signature
