I remember I had lots of problems with JVCL which constists of many units and packages. Initially all the runtime units were in a single directory, and everything worked fine. But the more units I added compilation become more and more complex, it only worked when I compiled them in a given order, and maintainance become a nightmare. Martin finally told me to separate the code into individual folders, all the units of package 1 go into folder 1, the units of package 2 to folder 2 etc. I also separated the output folders, i.e. package 1 compiles to lib/package1, package 2 to lib/package2 etc. This way the compilation issues could be solved. There is still a "duplicate unit" message sometimes.
lainz, having the packages in several repositories has no effect on the compilation issues when you merge both repositiories to the same folder on the compiling machine.