Although your deck is 480m long, but the length is broken up into a number of analytical members of much shorter length. For example if you look at the first load item under you load case 2, the loading is specified as
LOAD 2 LOADTYPE Live TITLE SUPER IMPOSED DEAD LOAD
MEMBER LOAD
2409 2414 UNI GY -1.47 0 480
…
As you can see, the uniformly distributed load has been applied to members 2409 and 2414 whose individual lengths are only 2m. So when you specify a d2 value of 480m, you are loading these members much beyond their actual lengths and hence you are getting the warnings. Instead you should load all the members along that line, that collectively form the girder, with the same uniformly distributed load to ensure that the entire girder length of 480 m is loaded. The loads defined within your load cases 2 and 3 had the issue. A modified file with the correction is uploaded for your reference.
(Please visit the site to view this file)