BDE 5 Index problem

I have just updated the DBE to version 5 from 4.51, and I am now
starting to experience some problems.
I have created three alias called
debug           D:\Dephi Files\Task
Alpha           C:\TaskMgr
Beta            C:\Program Files\TaskMgr

DeBug is used for debugging code in the Delphi IDE
Alpha is a copy of the latest working version that I use.
Beta is of testing the latest copy in InstallShiled for use to
distribute around the department.

Each of these aliases is set to use the FoxPro driver

Type                    Standard
Default Driver          FoxPro
Enable BCD              False
Path                    as above

Every thing seems to work ok, with the tables and indexes already in
use, but if an index file or table get deleted then the program will
re build these, but this is were the problems start.
It wants to use Dbase MDX format for the Index creates a MDX file and
then says that the index does not exist because it should be looking
for a CDX file.

Are there any Idlers on solving this problem?

Can I program the BDE from with in my application, so that the user
dose not have to use the BDE Admin program, and if that do will not
damage any information held in there for this application.
i.e. at run time the program will set all the parameters for the BDE.

Thank you for any help