TzahiG
It is difficult to comment on most of these issues without seeing the data and what you're using for the reference material values. If you're using WC1 as the primary, I believe it has variable common Pb, so U-Pb common approach or VizualAge UcomPbine would need to be used. If you're using NIST as the primary, I believe people do an offline correction to compensate for differences between the glass and carbonate (I might be wrong about this...). If you can share the raw data+logs and/or pxp file, as well as your reference material files with the support email, I'll have a closer look.
All the best,