I must agree that this sounds like a RAM problem. Selective cartridge failure can be attributed to how that cart program operates when there is an absence of RAM after $3FFF.
My first Atari was a 600XL with the memory expander module (back in 1985). After a number of years of use and transporting I would occasionally encounter a bad connection between the computer and module. This resulted in the absence of the extra RAM.
Regardless of the type of memory upgrade you have, suggest using the in-built self test function (hold down option at powerup, no cartridges) and select the memory test. This will let you know if your memory upgrade is letting you down. Note that if you enter the self test mode from basic by typing 'BYE' you will never see 48k of ram since the basic rom is occupying the last 8 kilobytes.
As an aside, there is a disk that PAGE 6 magazine used to sell containing some digitized music demos. This disk did not work on my XEGS. At first I suspected the XEGS and examined the circuitry intently but subsequently could not fault. It then occurred to me that the XEGS was not necessarily 100% hardware compatible with an XL. I tried the disk with my XL and it worked fine. After examining the machine code I discovered that the author had skipped convention when using register $D301 for bank switching. Instead of loading the register and then manipulating the appropriate bit(s), the author loaded the accumulator with a specific byte and stored it into $D301. From memory there was one or two bits set to zero that should have been set to on. Moral of the story is to question the premise of your conclusions! I was so close to dismantling my XEGS.