Typically the electric utilities want to save money & install 2 bank setup (open wye-open delta) instead of 3-bank setup. So, you have 2 transfomers bank, and the 3rd leg is man-made phase. If this is the case, then phase-to- phase reading is the correct way. Depending on transformer configuration, you may read 240volts phase-to-phase, or 120Volts on 2 legs, and wild leg reads 208volts nominal voltage, which is fine. With utility voltage regulators on utlity set at 125% to support with facility voltage drop you may read slightly higher reading i.e. 215volts.
Regarding troubleshooting machine that utilizes open delta, you probaly want to monitor the incoming line voltage to establish a baseline (i.e. monitor for voltage sags, swells, transients that cause problem), and check equipment-system grounding to bad or lose connection; and to ensure compliance with NEC Article 250. Last but not least, on open wye-open delta configuration with one dummy phase or man made phase, the sensitive electronics are susseptible to voltage fluctuations, and any system fault on utility lines will cause voltage surge inside the facility. If this is the case, installing 3-phase xfmr bank would be one solution, and this modification will have other consequences or wiring changes as well. Not knowing exactly what type of problems or issues your machine is experiencing its difficult to help with solutions.