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It may be coincidence, but the last time when there was significant freeze (around 2 minutes) I noticed that in the dmesg log there is timeout message from the samba mounts for the same amount of time.

[282179.691831] CIFS VFS: Server has not responded in 120 seconds. Reconnecting...
[282197.036283] CIFS VFS: Free previous auth_key.response = ffff971f09be9900
[283033.137624] pci_bus 0000:0b: Allocating resources
[283033.137650] pci 0000:00:1e.0: PCI bridge to [bus 0b]
[283033.137654] pci 0000:00:1e.0:   bridge window [io  0x8000-0x8fff]
[283033.137661] pci 0000:00:1e.0:   bridge window [mem 0xf7200000-0xf73fffff]