Just curious ... when trying to connect with (db)isql, are you doing this from the server where the ASE is running, or from another machine on the network? [If from another machine on the network, have you verified that sql.ini entries match on both machines?]
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It sounds like you may have a couple different (possibly unrelated) issues ... you can connect to the first ASE instance with (db)isql, but not so with the second ASE ... the first ASE instance has JS-related connectivity issues, while the second ASE instance appears to be cpu bound during startup.
For this latest/second ASE instance (cpu bound), have you perused the ASE errorlog for any messages of interest? Does this ASE instance show the same cpu bound issues each time it's started, and does the cpu usage ever go down after awhile?