Hello,
Just to let you know I ended up implementing my own Batch Least Squares method and the covariances I get from Orekit are of similar order to the ones that I get- so it seems this is the kind of change that one should expect! Still not sure what happened with the MEME to TEME conversion though- but I ended up just doing everything in MEME to get around this.
Anyways thanks for your help.
Best,
Charles