If you want to achieve what you want (having the RTC working even when the main power supply is off BUT with VBAT connected), you have to use the LSE. The fact that VBAT is connected allows you to keep the RTC value before shutting down the main power supply but here, the fact that you are using the LSI power off the RTC peripheral, that's why its value doesn't change. The shutdown mode is reached when you power off your system (even if you have VBAT connected), which is your case. Since you are using the LSI, the lowest power mode achievable for your RTC peripheral is the Standby mode.
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