I am not able to reproduce.
1. With this structure I do not see an issue.
M1 (multiple)
eqS1 (equation) (hidden) {S1=if(M1_SQ001=="Y" OR M1_SQ004=="Y",1,2)}
S1 (single) (hidden) answer option 1: proceed, 2: screenout
and quota: S1==2
2. It is not necessary to use the single punch question.
You may do it like this
M1 (multiple)
eqS1 (equation) (hidden) {if(M1_SQ001=="Y" OR M1_SQ004=="Y",1,2)}
and the quota on the equation: eqS1==2
Refer to the manual:
www.limesurvey.org/manual/Survey_quotas#..._other_question_type
So this is up to you.
And if there are more questions you are asked to send a lss export of this part of your survey.
Joffm