Check for " -ffunction-sections -fdata-sections " in the compile options, and "--gc-sections" in the link options. Arduino has become very dependent on these (which cause unreferenced functions and data to be omitted in the link phase) if you want reasonably sized sketches.
Do a verbose compile in the IDE, and make sure you know what ALL the switches provided to the compiler/etc actually do, before omitting them from other IDEs' configs...