With FG 3.0 separating the 3.5e and PFRPG into 2 different rulesets the character converter will only recognize PFRPG campaigns in the new FG 3.0 format. You need to open the old 3.5e PF campaign first so that Fantasy Grounds will convert it to the PFRPG ruleset - you get a message the first time you open the campaign letting you know that it has been converted to PFRPG. Once this has been done the campaign should appear for PFRPG in the character converter.

