The ICE errors may be the result of the original setup, however it is possible that the installscript msi conversion process generated the ICE error, due to the general nature of repackaging. However, any ICE errors generated by the InstallScript MSI conversion will be no different than if you had just used the standard repackaging process. In other words, the Installscript MSI conversion feature should never leave you worse off than if you had used the standard repackaging process instead.
The level of concern you should have for these errors would be the same as if you had just done the standard repackaging process instead--it varies depending upon what errors they are and what requirements you have of your setups on your end.
Mark