The exact cause remains a bit unclear. On the one hand, Nina Melis suggests that the problem may be specific to certain third-party schemes. For example, she found that she only had the problem when using the Lounge Lizard scheme (a MacUser Winning Scheme). On the other hand, Tom Rademacher reports that the problem persisted no matter which of over 20 different schemes he tried. Only reverting back to Kaleidoscope 1.5.1 prevented the errors.
In either case, consider getting SchemeChecker to check your third-party schemes. As noted by the author, Sven Berg Ryen, "Anybody can now make their own schemes, but unfortunately, not all scheme designers are careful enough to set all the required "System Heap" and "Purgeable" bits of their schemes' resources correct. SchemeChecker is a small, useful utility that makes it possible to check the schemes for errors." The current beta version (1.0b7) requires HyperCard to work.
SchemeChecker can't fix errors but it can alert you to them. Sven recommends not trying to fix schemes yourself unless you know for sure what you are doing; instead, contact the author of the scheme about the problem. A future version (due some time in June) will have an option to correct the errors found by SchemeChecker.