Although mobile Java code is frequently executed on many wireless devices, the susceptibility to electromagnetic (EM) attacks is largely unknown. If analysis of EM waves emanating from the wireless device during a cryptographic computation does leak sufficient information, it may be possible for an attacker to reconstruct the secret key. Despite the complexities of a Java-based PDA device, this paper presents a new phase-based technique for aligning EM frames for subsequent time-based DEMA which extracts the secret key. Unlike previous research the new technique does not require perfect alignment of EM frames and demonstrates robustness in the presence of a complex embedded system. This research is important for future wireless embedded systems which will increasingly demand higher levels of security.