Dear Jayakumar Kandathi Purayil , the behavior is far from being unique because you have specified the two sets of batteries giving their capacity, that does not give real indication of the internal resistance. Then, the real internal resistance depends also on thee existing state of charge of each and the health status (e.g. aged battery). If each set is charged separately, then as batteries are series connected the current flow is clear: all see the same current.

Putting batteries in parallel for charging is not a good idea, as the behavior may be quite strange, with unequal share of the charging current, that will not be stable: during charge there are changes of internal resistance. In addition if you do not protected the two sets with a series diode , when you connect them in parallel you will have a sudden discharge of current from one set onto the other, depending on the total voltage at the their terminals.

I'd agree with the point made by Andrea regarding internal resistance, not capacity being the significant factor in the current that flows through the two strings of batteries.

Also, is this a practical experiment that you're planning to try? If so, be aware that each of the 18 batteries in each string will not necessarily charge up at the same time. Your (12 * 18)= 216+ Volt charger won't know that you are potentially overcharging individual batteries. Some could be at 8V, others at 16V and the string voltage could still be 216V. It's safer to keep this as a hypothetical question!