Baseline shift issues on export

I am new to FontSelf and would appreciate some advice. I have built a fontset in Illustrator and imported the glyphs into FontSelf. Spent a lot of time adjusting baseline, etc. When I export the font, several characters are sitting well above baseline. I can adjust this by moving the characters below the baseline and re-exporting, but that does not seem efficient. Are there any suggestions for best practice in getting font glyphs to stay aligned on export?
Thanks.

Hi, please update some screenshots on both apps to understand the issue. You can also send files at hello@fontself.com for closer inspection.