Try some previous version, this mining software have many bugs for very long time without fixing.
Try different versions - some algo combinations for dual mining may be broken in different versions.
You could be kind enough and write down here those bugs ?
--multi-algorithm-job-mode 3 - broken (at least for nvidia) at least from version 2.3.7.
Latest few versions - MinotaurX broken, yespowerltncg - broken, yespower and some other cpu algo - something wrong when working with intel cpu's, especially with E Xeon's v3 v4 versions and N100-N300 cpu's - miner show good hashrate, but too low numbers of found shares, for example: yespower, Xeon E2650 V4 - hashrate ~ 1300h/s, on pool hashrate - 130 h/s.
--multi-algorithm-job-mode 3 is not broken, also its not a gpu dependent thing. Write down the example that's not working for you, then i might be able to test.
Im aware of some yespower derivates broken - broke in last version - not for very long time as you wrote.
Also the miner vs pool hr on some algorithms fixed in v2.4.5 - it is in the release notes.
+ Fixed an issue that caused higher difficulty to be used than what the pool sent - on some algorithms, introduced in previous version