Talking through this stuff often helps, in my experience of doing tech support. Hm. What if you made a converted to XLS copy of the other ODS document you were pasting from? See if the charts are okay in that, then copy-paste them into your new Excel document where those charts were disappearing? I don't know exactly what you're doing with the data, so I don't know if it's actually a viable option, but it seems like it might be a workaround.

Also, this is a weird thing, so it might be worth submitting a bug report to the open office community if you feel up to it sooner or later-- it might mean that they will later figure out what in the code is causing this wackiness to occur.