[ARCHIVE ANSWER]
Unless DPS has a new system, he was lying to you. The only "flagging" capability would be to report you to EPIC (El Paso Intelligence Center) which keeps records of smuggler activities. Having $5,000 cash on you with no history of smuggling is not enough to be placed in EPIC.
I am only aware of DPS having access to your criminal history, driver's license, and auto information through NCIC and TCIC (National Crime Intelligence Center and Texas Crime Intelligence Center.) Neither of these systems has a place for officers to "enter" suspicious activity.
It sounds to me like you are safe.