I don’t know about EEGLAB, but maybe there’s some differences in terms of the mixing and unmixing matrices?
What’s saved in the Channel File in BST, from what I understand, is the unmixing matrix W, that can be used to estimate the ICA time-series W * X where X is the channel data. The topographies that are displayed must be the mixing matrix that’s obtained by inverting as pinv(W) , not sure where in the code (?). If you load from EEGLAB the mixing matrix instead, this would lead to differences in topographies and time-series. Does that make sense?