It's impossible to say anything for certain because you haven't provided anywhere near enough information. However, this very likely isn't about the IDE's behavior. It's about the differences in the things that are bundled with each version of the IDE:
- Arduino AVR Boards core library
- Arduino AVR Boards platform bundled libraries
- Arduino AVR Boards toolchain
- IDE built-in libraries
If you want more help, you're going to need to provide:
- the sketch
- instructions for installing any additional libraries we might need for compiling your sketch
- the verbose output from compiling the sketch using the old version of the IDE
- the verbose output from compiling the sketch using the new version of the IDE