Were the seeds initially created using Electrum or were they imported seeds from another wallet? If they were Electrum generated seeds, then they would be "versioned", so would automatically restore using the correct derivation path and script type.
If they were imported seeds that were generated by another wallet, are the addresses that are generated in Electrum of the same type as they used to be? ie. "1"-type, "3"-type or "bc1"-type addresses? Or has this now changed? ie. they were "1"-type addresses, but now start with "bc1"? If they address type has changed, then the derivation path and/or script type is likely incorrect and Electrum is generating the wrong addresses.
Another likely reason is that you "extended the seed with custom word(s)" when you originally setup your wallet... if you did add an extra word or words (aka a "Seed passphrase"), then you must use the same extra words when restoring your wallet, otherwise the wallet generated will be completely different.
Finally, and less likely... is that the seed you have for your 2nd wallet is just wrong. Have you ever used this seed to restore your wallet before? Or is this the first time you have used it? If you haven't tested it before, it's possible that you have written down a "valid" seed, but one that was for a different wallet

It's not common, but it does happen... although it is more common with the desktop version.