GEDCOM does not move pictures, never has, never will.
What a GEDCOM can do is move the link of the location of the picture on your hard drive from one product to another. If the location of the picture is not on your hard drive or the location path in the GEDCOM is incomplete then the path will never work and the reading program will not find the picture.
As far as NOTEs, it kind of depends on what kind of NOTE it is and how each of the products support NOTEs.
Since most programs don't support GEDCOM correctly, data is always lost. if each of the program's create the same type of NOTE data they should be read by the other.
So the problem could be several different things depending on what each program can generate and what they expect and read. Just because they once worked does not mean they will now work if you have loaded updates of either program. Software companies occasionally break their code or remove features.
Also check to see if the programs have any parameters to their export and import processes you may need to experiment with the options to create something that increases compatability.
Sorry to say that while some people will say that GEDCOM is old wHich in this case is not true, BUT rather it is usually the fault of the programs not creating good GEDCOM or not reading GEDCOM correctly.
I don't use ACOM (ancestry.com) or Rootsweb because they don't support GEDCOM correctly and my database is GEDCOM compliant.