Forced hibernate is too early

Does powermanager properly detects both batteries?
Is one battery has much less capacity as the other?
Can you attach output of "lshal" when both batteries are attached?

Interesting data from lshal:

BAT1:
  battery.remaining_time = 1031 (0x407) (int)
  battery.charge_level.percentage = 100 (0x64) (int)
  battery.charge_level.rate = 5162 (0x142a) (int)
  battery.charge_level.last_full = 1479 (0x5c7) (int)
  battery.charge_level.current = 1479 (0x5c7) (int)
  battery.rechargeable.is_discharging = true (bool)
  battery.rechargeable.is_charging = false (bool)

BAT2:
  battery.remaining_time = 7627 (0x1dcb) (int)
  battery.charge_level.percentage = 100 (0x64) (int)
  battery.charge_level.rate = 5189 (0x1445) (int)
  battery.charge_level.last_full = 10994 (0x2af2) (int)
  battery.charge_level.current = 10994 (0x2af2) (int)
  battery.rechargeable.is_discharging = true (bool)
  battery.rechargeable.is_charging = false (bool)

As you can see, both batteries are fully charged and both are discharging (this is different than on my HP nw8240 where external battery is discharged first). You may also notice that two batteries have very different capacity (1479 vs. 10994) which impacts very different remaining time (1031 vs. 7627).
It is very likely that first battery is old and therefore cannot provide full capacity anymore. This is why you may get less juice out than you would anticipate.

On the other hand, you can now configure in power-manager when the laptop critical action should be performed - the default is 5 min and this may be too high for your laptop (I have it on 0 min as this is still enough juice to properly hibernate my laptop)

That's not the issue. Both batteries are of equal age.
They discharge at the same time. So in theory they should run out of juice at the same time.

However they charge sequentially, first the smaller main battery, then the juicy big one. So if I unplug the laptop after first battery finished charging, the second one will run out of juice while the first one still has some time left. The laptop should not hibernate if only one battery is out of juice.

Can you provide "lshal" at that the point when I battery is empty and other is discharging?

Providing output of "lshal -m" when first battery becomes empty would be even better.

See bug 60442 for more analysis.

It probably makes sense to fix this for Edgy by changing CHARGE_LEVEL_THRESHOLD to much lower value (5-10%?).

Fix to workaround this issue was committed in KDE SVN: r597776

Change CHARGE_LEVEL_THRESHOLD to 10% (was 50%) to better workaround acpi
issue when remaining_time is not reported correctly.
Also use threshold for battery low notification warning (do not issue low
warning if battery level above 10%)