Opting Out of EPS
Opting out of EPS will depend not only on the salary but also on the date of joining the Fund. If your first employment was after 1st September 2014 and the PF qualifying salary at the time of joining the first organization was above Rs 15,000, then your opting out of EPS was correct. Actually, it is not opting out, but you should have been excluded from EPS. Now, the second company has contributed to EPS either by mistake or due to a lack of knowledge of the law. They should not have contributed to EPS but should have contributed their share exclusively to EPF without bifurcating it as 8.33% to EPS and the remaining 3.67% to EPF.
Informing the Third Company
When you join a third company, you should inform the Personnel Officer that you are an existing member of EPF and there is no way you could be excluded from PF. Naturally, if the third company has fewer than 20 employees, that establishment will not have PF registration. In such cases, you will have to wait until the establishment gets coverage first and then you can be covered by EPF.
Correcting Contributions
Before that, you need to get the contributions made by the second company corrected. Otherwise, when you go for the withdrawal of PF or transfer the PF, the system will reject it, stating that your first company did not contribute to EPS or the second company did contribute to EPS, etc. Nowadays, the main objective of EPFO is the rejection of claims. Therefore, you have to correct the second company's contributions and divert the funds from EPS to EPF. It is just a reconciliation and transfer of funds for the EPFO, but they will not do it by themselves until the member reminds them of their duties every day!